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Squashed 'phreeqcpp/' changes from 93ab5c9..82515f7

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82515f7 Merge remote-tracking branch 'origin/master'
1cc4fa0 fix phi for water at high TP. Tony May, 2023
275b340 Tony's changes May 5 and 7.
0fb2509 cleaned up compiler warnings. removed math.h. cleaned up NAN

git-subtree-dir: phreeqcpp
git-subtree-split: 82515f7fecada9be373fd832dd0c5cdf53c79da7
This commit is contained in:
Darth Vader 2023-05-26 04:27:58 +00:00
parent dc26aa2a8f
commit 050663209b
19 changed files with 78 additions and 125 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
ChartHandler.cpp
View File

@ -170,18 +170,14 @@ ChartHandler::End_timer()
io->error_flush(); io->error_flush();
} }
} }
size_t i(0), i2(0);
for ( ; it != chart_map.end(); it++) for ( ; it != chart_map.end(); it++)
{ {
i = 0;
it->second->Rate_free(); it->second->Rate_free();
if (it->second->Get_form_started()) if (it->second->Get_form_started())
{ {
#if defined(__cplusplus_cli) #if defined(__cplusplus_cli)
while (0 != System::Threading::Interlocked::CompareExchange(it->second->usingResource, 6, 0)) while (0 != System::Threading::Interlocked::CompareExchange(it->second->usingResource, 6, 0))
{ {
//if (i > max_tries) break;
i++;
System::Threading::Thread::Sleep(60); System::Threading::Thread::Sleep(60);
} }
#endif #endif
@ -191,12 +187,8 @@ ChartHandler::End_timer()
int n = System::Threading::Interlocked::Exchange(it->second->usingResource, 0); int n = System::Threading::Interlocked::Exchange(it->second->usingResource, 0);
assert(n == 6); assert(n == 6);
#endif #endif
i2 = 0;
while (it->second->Get_done() != true) while (it->second->Get_done() != true)
{ {
//if (i2 > max_tries) break;
i2++;
#if defined(__cplusplus_cli) #if defined(__cplusplus_cli)
System::Threading::Thread::Sleep(60); System::Threading::Thread::Sleep(60);
#endif #endif
@ -225,7 +217,6 @@ ChartHandler::dump(std::ostream & oss, unsigned int indent)
std::map<int, ChartObject *>::iterator it = this->chart_map.begin(); std::map<int, ChartObject *>::iterator it = this->chart_map.begin();
for ( ; it != chart_map.end(); it++) for ( ; it != chart_map.end(); it++)
{ {
size_t i = 0;
it->second->dump(oss, indent); it->second->dump(oss, indent);
} }
return true; return true;

1
ChartObject.cpp
View File

@ -11,7 +11,6 @@
#include "ChartObject.h" #include "ChartObject.h"
#include "Parser.h" #include "Parser.h"
#include <fstream> #include <fstream>
//#include <math.h>
#include <cmath> #include <cmath>
#include <iomanip> #include <iomanip>
#include "phqalloc.h" #include "phqalloc.h"

11
PBasic.cpp
View File

@ -1558,6 +1558,9 @@ listtokens(FILE * f, tokenrec * l_buf)
case tokt_sc: case tokt_sc:
output_msg("T_SC"); output_msg("T_SC");
break; break;
case tokf_visc:
output_msg("F_VISC");
break;
case toktc: case toktc:
output_msg("TC"); output_msg("TC");
break; break;
@ -3904,6 +3907,13 @@ factor(struct LOC_exec * LINK)
} }
break; break;
case tokf_visc:
{
const char* str = stringfactor(STR1, LINK);
n.UU.val = (parse_all) ? 1 : PhreeqcPtr->calc_f_visc(str);
}
break;
case toktc: case toktc:
{ {
n.UU.val = PhreeqcPtr->tc_x; n.UU.val = PhreeqcPtr->tc_x;
@ -7518,6 +7528,7 @@ const std::map<const std::string, PBasic::BASIC_TOKEN>::value_type temp_tokens[]
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("surf", PBasic::toksurf), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("surf", PBasic::toksurf),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("sys", PBasic::toksys), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("sys", PBasic::toksys),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("t_sc", PBasic::tokt_sc), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("t_sc", PBasic::tokt_sc),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("f_visc", PBasic::tokf_visc),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("tc", PBasic::toktc), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("tc", PBasic::toktc),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("time", PBasic::toktime), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("time", PBasic::toktime),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("title", PBasic::toktitle), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("title", PBasic::toktitle),

2
PBasic.h
View File

@ -7,7 +7,6 @@
#include <stdio.h> #include <stdio.h>
#include <limits.h> #include <limits.h>
#include <ctype.h> #include <ctype.h>
//#include <math.h>
#include <cmath> #include <cmath>
#include <setjmp.h> #include <setjmp.h>
#include "phrqtype.h" #include "phrqtype.h"
@ -338,6 +337,7 @@ public:
toktotmol, toktotmol,
toktotmoles, toktotmoles,
toktrim, toktrim,
tokf_visc,
tokviscos, tokviscos,
tokviscos_0, tokviscos_0,
tokvm, tokvm,

1
Phreeqc.h
View File

@ -996,6 +996,7 @@ public:
int reformat_surf(const char* comp_name, LDBLE fraction, const char* new_comp_name, int reformat_surf(const char* comp_name, LDBLE fraction, const char* new_comp_name,
LDBLE new_Dw, int cell); LDBLE new_Dw, int cell);
LDBLE viscosity(void); LDBLE viscosity(void);
LDBLE calc_f_visc(const char *name);
LDBLE calc_vm_Cl(void); LDBLE calc_vm_Cl(void);
int multi_D(LDBLE DDt, int mobile_cell, int stagnant); int multi_D(LDBLE DDt, int mobile_cell, int stagnant);
LDBLE find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant); LDBLE find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant);

5
SolutionIsotope.cxx
View File

@ -67,12 +67,7 @@ cxxSolutionIsotope::dump_xml(std::ostream & s_oss, unsigned int indent) const
s_oss << indent1; s_oss << indent1;
s_oss << "iso_ratio=\"" << this->ratio << "\"" << "\n"; s_oss << "iso_ratio=\"" << this->ratio << "\"" << "\n";
#ifdef NPP
if (!isnan(this->ratio_uncertainty))
#else
//if (this->ratio_uncertainty != NAN)
if (!std::isnan(this->ratio_uncertainty)) if (!std::isnan(this->ratio_uncertainty))
#endif
{ {
s_oss << indent1; s_oss << indent1;
s_oss << "iso_ratio_uncertainty=\"" << this-> s_oss << "iso_ratio_uncertainty=\"" << this->

64
basicsubs.cpp
View File

@ -1252,6 +1252,24 @@ calc_t_sc(const char *name)
return (-999.99); return (-999.99);
} }
/* ---------------------------------------------------------------------- */
LDBLE Phreeqc::
calc_f_visc(const char *name)
/* ---------------------------------------------------------------------- */
{
char token[MAX_LENGTH];
class species *s_ptr;
if (print_viscosity)
{
strcpy(token, name);
s_ptr = s_search(token);
if (s_ptr != NULL)
return s_ptr->dw_t_visc;
}
return 0;
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
LDBLE Phreeqc:: LDBLE Phreeqc::
equi_phase(const char *phase_name) equi_phase(const char *phase_name)
@ -1599,12 +1617,7 @@ get_calculate_value(const char *name)
calculate_value_ptr->name); calculate_value_ptr->name);
error_msg(error_string, STOP); error_msg(error_string, STOP);
} }
#ifdef NPP
if (isnan(rate_moles))
#else
//if (rate_moles == NAN)
if(std::isnan(rate_moles)) if(std::isnan(rate_moles))
#endif
{ {
error_string = sformatf( "Calculated value not SAVEed for %s.", error_string = sformatf( "Calculated value not SAVEed for %s.",
calculate_value_ptr->name); calculate_value_ptr->name);
@ -1762,18 +1775,17 @@ LDBLE Phreeqc::
pr_pressure(const char* phase_name) pr_pressure(const char* phase_name)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
{ {
int l;
class phase* phase_ptr = phase_bsearch(phase_name, &l, FALSE);
if (phase_ptr == NULL)
{
error_string = sformatf("Gas %s, not found.", phase_name);
warning_msg(error_string);
return (1e-99);
}
cxxGasPhase* gas_phase_ptr = use.Get_gas_phase_ptr(); cxxGasPhase* gas_phase_ptr = use.Get_gas_phase_ptr();
if (gas_phase_ptr != NULL) if (gas_phase_ptr != NULL)
{ {
int l;
class phase* phase_ptr = phase_bsearch(phase_name, &l, FALSE);
if (phase_ptr == NULL)
{
error_string = sformatf("Gas %s, not found.", phase_name);
warning_msg(error_string);
return (1e-99);
}
for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++) for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++)
{ {
const cxxGasComp* gas_comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]); const cxxGasComp* gas_comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]);
@ -1792,6 +1804,10 @@ pr_pressure(const char* phase_name)
} }
} }
} }
else if (phase_ptr->in != FALSE && phase_ptr->pr_in)
{
return phase_ptr->pr_p;
}
return(0.0); return(0.0);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1807,35 +1823,35 @@ LDBLE Phreeqc::
pr_phi(const char *phase_name) pr_phi(const char *phase_name)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
{ {
cxxGasPhase* gas_phase_ptr = use.Get_gas_phase_ptr();
if (gas_phase_ptr != NULL)
{
int l; int l;
class phase* phase_ptr = phase_bsearch(phase_name, &l, FALSE); class phase* phase_ptr = phase_bsearch(phase_name, &l, FALSE);
if (phase_ptr == NULL) if (phase_ptr == NULL)
{ {
error_string = sformatf( "Gas %s, not found.", phase_name); error_string = sformatf( "Gas %s, not found.", phase_name);
warning_msg(error_string); warning_msg(error_string);
return (1e-99); return (1e-99);
} }
for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++) cxxGasPhase* gas_phase_ptr = use.Get_gas_phase_ptr();
if (gas_phase_ptr != NULL)
{ {
for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++)
{
const cxxGasComp* gas_comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]); const cxxGasComp* gas_comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]);
int j; int j;
class phase* phase_ptr_gas = phase_bsearch(gas_comp_ptr->Get_phase_name().c_str(), &j, FALSE); class phase* phase_ptr_gas = phase_bsearch(gas_comp_ptr->Get_phase_name().c_str(), &j, FALSE);
if (phase_ptr == phase_ptr_gas) if (phase_ptr == phase_ptr_gas)
{ {
if (gas_phase_ptr->Get_pr_in()) if (gas_phase_ptr->Get_pr_in())
{ return phase_ptr->pr_phi;
return phase_ptr->pr_phi;
}
else else
{
return gas_comp_ptr->Get_phi(); return gas_comp_ptr->Get_phi();
}
} }
} }
} }
else if (phase_ptr->in != FALSE && phase_ptr->pr_in)
{
return phase_ptr->pr_phi;
}
return (1.0); return (1.0);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
cl1.cpp
View File

@ -1,6 +1,5 @@
#include <stdio.h> #include <stdio.h>
#include <string.h> #include <string.h>
//#include <math.h>
#include <cmath> #include <cmath>
#include <stdlib.h> #include <stdlib.h>
#include "Phreeqc.h" #include "Phreeqc.h"

1
common/Utils.cxx
View File

@ -10,7 +10,6 @@
#include "Utils.h" #include "Utils.h"
#include "Parser.h" #include "Parser.h"
#include "float.h" #include "float.h"
//#include <math.h>
#include <cmath> #include <cmath>
#if defined(PHREEQCI_GUI) #if defined(PHREEQCI_GUI)

1
gases.cpp
View File

@ -607,6 +607,7 @@ calc_PR(void)
phi = B_r * (rz - 1) - log(rz - B) + A / (2.828427 * B) * (B_r - 2.0 * phase_ptr->pr_aa_sum2 / a_aa_sum) * phi = B_r * (rz - 1) - log(rz - B) + A / (2.828427 * B) * (B_r - 2.0 * phase_ptr->pr_aa_sum2 / a_aa_sum) *
log((rz + 2.41421356 * B) / (rz - 0.41421356 * B)); log((rz + 2.41421356 * B) / (rz - 0.41421356 * B));
//phi = (phi > 4.44 ? 4.44 : (phi < -3 ? -3 : phi)); //phi = (phi > 4.44 ? 4.44 : (phi < -3 ? -3 : phi));
phi = (phi > 4.44 ? 4.44 : (phi < -4.6 ? -4.6 : phi));
} }
else else
phi = -3.0; // fugacity coefficient = 0.05 phi = -3.0; // fugacity coefficient = 0.05

2
global_structures.h
View File

@ -715,6 +715,7 @@ public:
dw_a2 = 0; dw_a2 = 0;
dw_a_visc = 0; // viscosity correction of SC dw_a_visc = 0; // viscosity correction of SC
dw_t_SC = 0; // contribution to SC, for calc'ng transport number with BASIC dw_t_SC = 0; // contribution to SC, for calc'ng transport number with BASIC
dw_t_visc = 0; // contribution to viscosity
dw_corr = 0; // dw corrected for TK and mu dw_corr = 0; // dw corrected for TK and mu
erm_ddl = 0; // enrichment factor in DDL erm_ddl = 0; // enrichment factor in DDL
equiv = 0; // equivalents in exchange species equiv = 0; // equivalents in exchange species
@ -776,6 +777,7 @@ public:
LDBLE dw_a2; LDBLE dw_a2;
LDBLE dw_a_visc; LDBLE dw_a_visc;
LDBLE dw_t_SC; LDBLE dw_t_SC;
LDBLE dw_t_visc;
LDBLE dw_corr; LDBLE dw_corr;
LDBLE erm_ddl; LDBLE erm_ddl;
LDBLE equiv; LDBLE equiv;

24
inverse.cpp
View File

@ -3582,40 +3582,21 @@ check_isotopes(class inverse *inv_ptr)
i = ii; i = ii;
/* use inverse-defined uncertainties first */ /* use inverse-defined uncertainties first */
#ifdef NPP
if (j < inv_ptr->i_u[i].uncertainties.size()
&& !isnan(inv_ptr->i_u[i].uncertainties[j]))
#else
//if (j < inv_ptr->i_u[i].uncertainties.size()
// && inv_ptr->i_u[i].uncertainties[j] != NAN)
if (j < inv_ptr->i_u[i].uncertainties.size() if (j < inv_ptr->i_u[i].uncertainties.size()
&& !std::isnan(inv_ptr->i_u[i].uncertainties[j])) && !std::isnan(inv_ptr->i_u[i].uncertainties[j]))
#endif
{ {
kit->second.Set_x_ratio_uncertainty(inv_ptr->i_u[i].uncertainties[j]); kit->second.Set_x_ratio_uncertainty(inv_ptr->i_u[i].uncertainties[j]);
/* use solution-defined uncertainties second */ /* use solution-defined uncertainties second */
} }
#ifdef NPP
else if (inv_ptr->i_u[i].uncertainties.size() > 0
&& !isnan(inv_ptr->i_u[i].uncertainties[inv_ptr->i_u[i].uncertainties.size() - 1]))
#else
//else if (inv_ptr->i_u[i].uncertainties.size() > 0
// && inv_ptr->i_u[i].uncertainties[(size_t)inv_ptr->i_u[i].uncertainties.size() - 1] != NAN)
else if (inv_ptr->i_u[i].uncertainties.size() > 0 else if (inv_ptr->i_u[i].uncertainties.size() > 0
&& !std::isnan(inv_ptr->i_u[i].uncertainties[inv_ptr->i_u[i].uncertainties.size() - 1])) && !std::isnan(inv_ptr->i_u[i].uncertainties[inv_ptr->i_u[i].uncertainties.size() - 1]))
#endif
{ {
kit->second.Set_x_ratio_uncertainty(inv_ptr->i_u[i].uncertainties[inv_ptr->i_u[i].uncertainties.size() - 1]); kit->second.Set_x_ratio_uncertainty(inv_ptr->i_u[i].uncertainties[inv_ptr->i_u[i].uncertainties.size() - 1]);
/* use solution-defined uncertainties second */ /* use solution-defined uncertainties second */
} }
#ifdef NPP
else if (!isnan(kit->second.Get_ratio_uncertainty()))
#else
//else if (kit->second.Get_ratio_uncertainty() != NAN)
else if (!std::isnan(kit->second.Get_ratio_uncertainty())) else if (!std::isnan(kit->second.Get_ratio_uncertainty()))
#endif
{ {
kit->second.Set_x_ratio_uncertainty( kit->second.Set_x_ratio_uncertainty(
kit->second.Get_ratio_uncertainty()); kit->second.Get_ratio_uncertainty());
@ -3643,12 +3624,7 @@ check_isotopes(class inverse *inv_ptr)
} }
} }
} }
#ifdef NPP
if (isnan(kit->second.Get_x_ratio_uncertainty()))
#else
//if (kit->second.Get_x_ratio_uncertainty() == NAN)
if (std::isnan(kit->second.Get_x_ratio_uncertainty())) if (std::isnan(kit->second.Get_x_ratio_uncertainty()))
#endif
{ {
error_string = sformatf( error_string = sformatf(
"In solution %d, isotope ratio uncertainty is needed for element: %g%s.", "In solution %d, isotope ratio uncertainty is needed for element: %g%s.",

15
isotopes.cpp
View File

@ -900,12 +900,7 @@ punch_calculate_values(void)
calculate_value_ptr->name); calculate_value_ptr->name);
error_msg(error_string, STOP); error_msg(error_string, STOP);
} }
#ifdef NPP
if (isnan(rate_moles))
#else
//if (rate_moles == NAN)
if (std::isnan(rate_moles)) if (std::isnan(rate_moles))
#endif
{ {
error_string = sformatf( "Calculated value not SAVEed for %s.", error_string = sformatf( "Calculated value not SAVEed for %s.",
calculate_value_ptr->name); calculate_value_ptr->name);
@ -1134,12 +1129,7 @@ calculate_values(void)
calculate_value_ptr->name); calculate_value_ptr->name);
error_msg(error_string, STOP); error_msg(error_string, STOP);
} }
#ifdef NPP
if (isnan(rate_moles))
#else
//if (rate_moles == NAN)
if (std::isnan(rate_moles)) if (std::isnan(rate_moles))
#endif
{ {
error_string = sformatf( "Calculated value not SAVEed for %s.", error_string = sformatf( "Calculated value not SAVEed for %s.",
calculate_value_ptr->name); calculate_value_ptr->name);
@ -1202,12 +1192,7 @@ calculate_values(void)
calculate_value_ptr->name); calculate_value_ptr->name);
error_msg(error_string, STOP); error_msg(error_string, STOP);
} }
#ifdef NPP
if (isnan(rate_moles))
#else
//if (rate_moles == NAN)
if (std::isnan(rate_moles)) if (std::isnan(rate_moles))
#endif
{ {
error_string = sformatf( "Calculated value not SAVEed for %s.", error_string = sformatf( "Calculated value not SAVEed for %s.",
calculate_value_ptr->name); calculate_value_ptr->name);

5
kinetics.cpp
View File

@ -115,12 +115,7 @@ calc_kinetic_reaction(cxxKinetics *kinetics_ptr, LDBLE time_step)
kinetics_comp_ptr->Get_rate_name().c_str()); kinetics_comp_ptr->Get_rate_name().c_str());
error_msg(error_string, STOP); error_msg(error_string, STOP);
} }
#ifdef NPP
if (isnan(rate_moles))
#else
//if (rate_moles == NAN)
if (std::isnan(rate_moles)) if (std::isnan(rate_moles))
#endif
{ {
error_string = sformatf( "Moles of reaction not SAVEed for %s.", error_string = sformatf( "Moles of reaction not SAVEed for %s.",
kinetics_comp_ptr->Get_rate_name().c_str()); kinetics_comp_ptr->Get_rate_name().c_str());

1
prep.cpp
View File

@ -3997,6 +3997,7 @@ calc_PR(std::vector<class phase *> phase_ptrs, LDBLE P, LDBLE TK, LDBLE V_m)
phi = B_r * (rz - 1) - log(rz - B) + A / (2.828427 * B) * (B_r - 2.0 * phase_ptr->pr_aa_sum2 / a_aa_sum) * phi = B_r * (rz - 1) - log(rz - B) + A / (2.828427 * B) * (B_r - 2.0 * phase_ptr->pr_aa_sum2 / a_aa_sum) *
log((rz + 2.41421356 * B) / (rz - 0.41421356 * B)); log((rz + 2.41421356 * B) / (rz - 0.41421356 * B));
//phi = (phi > 4.44 ? 4.44 : (phi < -3 ? -3 : phi)); //phi = (phi > 4.44 ? 4.44 : (phi < -3 ? -3 : phi));
phi = (phi > 4.44 ? 4.44 : (phi < -4.6 ? -4.6 : phi));
//if (phi > 4.44) //if (phi > 4.44)
// phi = 4.44; // phi = 4.44;
} }

8
read.cpp
View File

@ -2699,7 +2699,7 @@ read_aq_species_vm_parms(const char* cptr, LDBLE * delta_v)
/* /*
* Read supcrt parms and Ionic strength terms * Read supcrt parms and Ionic strength terms
*/ */
for (j = 0; j < 11; j++) for (j = 0; j < 10; j++)
{ {
delta_v[j] = 0.0; delta_v[j] = 0.0;
} }
@ -2707,7 +2707,7 @@ read_aq_species_vm_parms(const char* cptr, LDBLE * delta_v)
/* Vmax, dmax... /* Vmax, dmax...
delta_v[10] = 999.0; delta_v[10] = 999.0;
delta_v[11] = 1.0; */ delta_v[11] = 1.0; */
j = sscanf(cptr, SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT , j = sscanf(cptr, SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT SCANFORMAT/* SCANFORMAT SCANFORMAT*/ ,
/* a1..a4 */ /* a1..a4 */
&(delta_v[0]), &(delta_v[1]), &(delta_v[2]), &(delta_v[3]), &(delta_v[0]), &(delta_v[1]), &(delta_v[2]), &(delta_v[3]),
/* wref */ /* wref */
@ -2715,9 +2715,9 @@ read_aq_species_vm_parms(const char* cptr, LDBLE * delta_v)
/* b_Av */ /* b_Av */
&(delta_v[5]), &(delta_v[5]),
/* c1..c4 */ /* c1..c4 */
&(delta_v[6]), &(delta_v[7]), &(delta_v[8]), &(delta_v[9]), &(delta_v[6]), &(delta_v[7]), &(delta_v[8]), &(delta_v[9])/*,
//vmP, exP //vmP, exP
&(delta_v[10]), &(delta_v[11])); &(delta_v[10]), &(delta_v[11])*/);
if (j < 1) if (j < 1)
{ {
input_error++; input_error++;

1
sundialsmath.cpp
View File

@ -59,7 +59,6 @@
#include <stdio.h> #include <stdio.h>
//#include <math.h>
#include <cmath> #include <cmath>
#include "sundialsmath.h" #include "sundialsmath.h"
#include "sundialstypes.h" #include "sundialstypes.h"

20
tidy.cpp
View File

@ -979,12 +979,7 @@ tidy_gas_phase(void)
error_msg(error_string, CONTINUE); error_msg(error_string, CONTINUE);
} }
/* calculate moles */ /* calculate moles */
#ifdef NPP
if (!isnan(gas_phase_ptr->Get_gas_comps()[j].Get_p_read()))
#else
//if (gas_phase_ptr->Get_gas_comps()[j].Get_p_read() != NAN)
if (!std::isnan(gas_phase_ptr->Get_gas_comps()[j].Get_p_read())) if (!std::isnan(gas_phase_ptr->Get_gas_comps()[j].Get_p_read()))
#endif
{ {
P += gas_phase_ptr->Get_gas_comps()[j].Get_p_read(); P += gas_phase_ptr->Get_gas_comps()[j].Get_p_read();
if (!PR) if (!PR)
@ -1013,12 +1008,7 @@ tidy_gas_phase(void)
*/ */
if (!gas_phase_ptr->Get_solution_equilibria()) if (!gas_phase_ptr->Get_solution_equilibria())
{ {
#ifdef NPP
if (!isnan(gas_phase_ptr->Get_gas_comps()[j].Get_p_read()))
#else
//if (gas_phase_ptr->Get_gas_comps()[j].Get_p_read() != NAN)
if (!std::isnan(gas_phase_ptr->Get_gas_comps()[j].Get_p_read())) if (!std::isnan(gas_phase_ptr->Get_gas_comps()[j].Get_p_read()))
#endif
{ {
P += gas_phase_ptr->Get_gas_comps()[j].Get_p_read(); P += gas_phase_ptr->Get_gas_comps()[j].Get_p_read();
if (!PR) if (!PR)
@ -1689,12 +1679,7 @@ tidy_ss_assemblage(void)
phase_ptr->moles_x = 0; phase_ptr->moles_x = 0;
phase_ptr->fraction_x = 0; phase_ptr->fraction_x = 0;
} }
#ifdef NPP
if (isnan(comp_ptr->Get_moles()))
#else
//if (comp_ptr->Get_moles() == NAN)
if (std::isnan(comp_ptr->Get_moles())) if (std::isnan(comp_ptr->Get_moles()))
#endif
{ {
input_error++; input_error++;
error_string = sformatf( error_string = sformatf(
@ -3021,12 +3006,7 @@ tidy_isotopes(void)
temp_iso.Set_total(0); temp_iso.Set_total(0);
temp_iso.Set_ratio(master[k]->isotope_ratio); temp_iso.Set_ratio(master[k]->isotope_ratio);
temp_iso.Set_ratio_uncertainty(master[k]->isotope_ratio_uncertainty); temp_iso.Set_ratio_uncertainty(master[k]->isotope_ratio_uncertainty);
#ifdef NPP
if (!isnan(master[k]->isotope_ratio_uncertainty))
#else
//if (master[k]->isotope_ratio_uncertainty != NAN)
if (!std::isnan(master[k]->isotope_ratio_uncertainty)) if (!std::isnan(master[k]->isotope_ratio_uncertainty))
#endif
{ {
temp_iso.Set_ratio_uncertainty_defined(true); temp_iso.Set_ratio_uncertainty_defined(true);
} }

31
transport.cpp
View File

@ -5963,10 +5963,10 @@ viscosity(void)
We use the harmonic mean of the Dw's, and the arithmetic mean of the z's, We use the harmonic mean of the Dw's, and the arithmetic mean of the z's,
both weighted by the equivalent concentration. both weighted by the equivalent concentration.
*/ */
LDBLE D1, D2, z1, z2, m_plus, m_min, eq_plus, eq_min, eq_dw_plus, eq_dw_min, t1, t2, ta; LDBLE D1, D2, z1, z2, m_plus, m_min, eq_plus, eq_min, eq_dw_plus, eq_dw_min, t1, t2, t3, fan = 1;
LDBLE A, psi, Bc = 0, Dc = 0, Dw = 0.0, l_z, f_z, lm, V_an, m_an, V_Cl, tc; LDBLE A, psi, Bc = 0, Dc = 0, Dw = 0.0, l_z, f_z, lm, V_an, m_an, V_Cl, tc;
m_plus = m_min = eq_plus = eq_min = eq_dw_plus = eq_dw_min = V_an = m_an = V_Cl = ta = 0; m_plus = m_min = eq_plus = eq_min = eq_dw_plus = eq_dw_min = V_an = m_an = V_Cl = 0;
tc = (tc_x > 200) ? 200 : tc_x; tc = (tc_x > 200) ? 200 : tc_x;
@ -5978,6 +5978,7 @@ viscosity(void)
continue; continue;
if (s_x[i]->Jones_Dole[0] || s_x[i]->Jones_Dole[1] || s_x[i]->Jones_Dole[3]) if (s_x[i]->Jones_Dole[0] || s_x[i]->Jones_Dole[1] || s_x[i]->Jones_Dole[3])
{ {
s_x[i]->dw_t_visc = 0;
t1 = s_x[i]->moles / mass_water_aq_x; t1 = s_x[i]->moles / mass_water_aq_x;
l_z = fabs(s_x[i]->z); l_z = fabs(s_x[i]->z);
if (l_z) if (l_z)
@ -5993,8 +5994,9 @@ viscosity(void)
s_x[i]->Jones_Dole[8] / exp(-s_x[i]->Jones_Dole[4] * 25.0); s_x[i]->Jones_Dole[8] / exp(-s_x[i]->Jones_Dole[4] * 25.0);
} }
// find B * m and D * m * mu^d3 // find B * m and D * m * mu^d3
Bc += (s_x[i]->Jones_Dole[0] + s_x[i]->dw_t_visc = (s_x[i]->Jones_Dole[0] +
s_x[i]->Jones_Dole[1] * exp(-s_x[i]->Jones_Dole[2] * tc)) * t1; s_x[i]->Jones_Dole[1] * exp(-s_x[i]->Jones_Dole[2] * tc)) * t1;
Bc += s_x[i]->dw_t_visc;
// define f_I from the exponent of the D * m^d3 term... // define f_I from the exponent of the D * m^d3 term...
if (s_x[i]->Jones_Dole[5] >= 1) if (s_x[i]->Jones_Dole[5] >= 1)
t2 = mu_x / 3 / s_x[i]->Jones_Dole[5]; t2 = mu_x / 3 / s_x[i]->Jones_Dole[5];
@ -6002,8 +6004,10 @@ viscosity(void)
t2 = -0.8 / s_x[i]->Jones_Dole[5]; t2 = -0.8 / s_x[i]->Jones_Dole[5];
else else
t2 = -1; t2 = -1;
Dc += (s_x[i]->Jones_Dole[3] * exp(-s_x[i]->Jones_Dole[4] * tc)) * t3 = (s_x[i]->Jones_Dole[3] * exp(-s_x[i]->Jones_Dole[4] * tc)) *
t1 * (pow(mu_x, s_x[i]->Jones_Dole[5])*(1 + t2) + pow(t1 * f_z, s_x[i]->Jones_Dole[5])) / (2 + t2); t1 * (pow(mu_x, s_x[i]->Jones_Dole[5])*(1 + t2) + pow(t1 * f_z, s_x[i]->Jones_Dole[5])) / (2 + t2);
s_x[i]->dw_t_visc += t3;
Dc += t3;
//output_msg(sformatf("\t%s\t%e\t%e\t%e\n", s_x[i]->name, t1, Bc, Dc )); //output_msg(sformatf("\t%s\t%e\t%e\t%e\n", s_x[i]->name, t1, Bc, Dc ));
} }
// parms for A... // parms for A...
@ -6023,13 +6027,11 @@ viscosity(void)
{ {
V_Cl = s_x[i]->logk[vm_tc]; V_Cl = s_x[i]->logk[vm_tc];
V_an += V_Cl * s_x[i]->moles; V_an += V_Cl * s_x[i]->moles;
ta += s_x[i]->moles;
m_an += s_x[i]->moles; m_an += s_x[i]->moles;
} }
else// if (s_x[i]->Jones_Dole[6]) else// if (s_x[i]->Jones_Dole[6])
{ {
V_an += s_x[i]->logk[vm_tc] * s_x[i]->Jones_Dole[6] * s_x[i]->moles; V_an += s_x[i]->logk[vm_tc] * s_x[i]->Jones_Dole[6] * s_x[i]->moles;
ta += s_x[i]->moles;
m_an += s_x[i]->moles; m_an += s_x[i]->moles;
} }
if (Dw) if (Dw)
@ -6064,23 +6066,24 @@ viscosity(void)
A = 0; A = 0;
viscos = viscos_0 + A * sqrt((eq_plus + eq_min) / 2 / mass_water_aq_x); viscos = viscos_0 + A * sqrt((eq_plus + eq_min) / 2 / mass_water_aq_x);
if (m_an) if (m_an)
{
V_an /= m_an; V_an /= m_an;
ta /= m_an;
}
if (!V_Cl) if (!V_Cl)
V_Cl = calc_vm_Cl(); V_Cl = calc_vm_Cl();
if (V_an && V_Cl && ta) if (V_an)
viscos += (viscos_0 * (2 - ta * V_an / V_Cl) * (Bc + Dc)); fan = 2 - V_an / V_Cl;
else //else
viscos += (viscos_0 * (Bc + Dc)); // fan = 1;
viscos += viscos_0 * fan * (Bc + Dc);
if (viscos < 0) if (viscos < 0)
{ {
viscos = viscos_0; viscos = viscos_0;
warning_msg("viscosity < 0, reset to viscosity of pure water"); warning_msg("viscosity < 0, reset to viscosity of pure water");
} }
for (i = 0; i < (int)this->s_x.size(); i++)
{
s_x[i]->dw_t_visc /= (Bc + Dc);
}
return viscos; return viscos;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
LDBLE Phreeqc:: LDBLE Phreeqc::