pyEQL 1.4.0rc9__cp312-cp312-macosx_10_13_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (491) hide show
  1. pyEQL/__init__.py +50 -0
  2. pyEQL/_phreeqc.cpython-312-darwin.so +0 -0
  3. pyEQL/activity_correction.py +879 -0
  4. pyEQL/database/geothermal.dat +5693 -0
  5. pyEQL/database/llnl.dat +19305 -0
  6. pyEQL/database/phreeqc_license.txt +54 -0
  7. pyEQL/database/pyeql_db.json +35607 -0
  8. pyEQL/engines.py +1153 -0
  9. pyEQL/equilibrium.py +227 -0
  10. pyEQL/functions.py +281 -0
  11. pyEQL/phreeqc/__init__.py +5 -0
  12. pyEQL/phreeqc/bindings.cpp +84 -0
  13. pyEQL/phreeqc/core.py +239 -0
  14. pyEQL/phreeqc/database/Amm.dat +1968 -0
  15. pyEQL/phreeqc/database/CMakeLists.txt +32 -0
  16. pyEQL/phreeqc/database/ColdChem.dat +267 -0
  17. pyEQL/phreeqc/database/Concrete_PHR.dat +158 -0
  18. pyEQL/phreeqc/database/Concrete_PZ.dat +195 -0
  19. pyEQL/phreeqc/database/Kinec.v2.dat +12039 -0
  20. pyEQL/phreeqc/database/Kinec_v3.dat +12159 -0
  21. pyEQL/phreeqc/database/Makefile.am +28 -0
  22. pyEQL/phreeqc/database/Makefile.in +530 -0
  23. pyEQL/phreeqc/database/PHREEQC_ThermoddemV1.10_15Dec2020.dat +12965 -0
  24. pyEQL/phreeqc/database/Tipping_Hurley.dat +4137 -0
  25. pyEQL/phreeqc/database/__init__.py +0 -0
  26. pyEQL/phreeqc/database/core10.dat +6824 -0
  27. pyEQL/phreeqc/database/frezchem.dat +634 -0
  28. pyEQL/phreeqc/database/iso.dat +7235 -0
  29. pyEQL/phreeqc/database/llnl.dat +19310 -0
  30. pyEQL/phreeqc/database/minteq.dat +5654 -0
  31. pyEQL/phreeqc/database/minteq.v4.dat +13212 -0
  32. pyEQL/phreeqc/database/phreeqc.dat +1972 -0
  33. pyEQL/phreeqc/database/phreeqc_rates.dat +3158 -0
  34. pyEQL/phreeqc/database/pitzer.dat +1044 -0
  35. pyEQL/phreeqc/database/sit.dat +14348 -0
  36. pyEQL/phreeqc/database/wateq4f.dat +4036 -0
  37. pyEQL/phreeqc/ext/README.md +10 -0
  38. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/CMakeLists.txt +476 -0
  39. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/INSTALL +302 -0
  40. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/IPhreeqc.rc +61 -0
  41. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/IPhreeqcConfig.cmake.in +4 -0
  42. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/Makefile.am +8 -0
  43. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/Makefile.in +816 -0
  44. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/aclocal.m4 +1217 -0
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  46. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/build/CMakeFiles/IPhreeqc.dir/src/CSelectedOutput.cpp.o +0 -0
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  48. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/build/CMakeFiles/IPhreeqc.dir/src/IPhreeqcLib.cpp.o +0 -0
  49. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/build/CMakeFiles/IPhreeqc.dir/src/IPhreeqc_interface_F.cpp.o +0 -0
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  371. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SelectedOutput.cpp +115 -0
  372. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SelectedOutput.h +209 -0
  373. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Serializer.cxx +213 -0
  374. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Serializer.h +42 -0
  375. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Solution.cxx +1795 -0
  376. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Solution.h +154 -0
  377. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SolutionIsotope.cxx +333 -0
  378. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SolutionIsotope.h +85 -0
  379. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/StorageBin.cxx +1507 -0
  380. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/StorageBin.h +141 -0
  381. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/StorageBinList.cpp +358 -0
  382. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/StorageBinList.h +81 -0
  383. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Surface.cxx +837 -0
  384. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Surface.h +108 -0
  385. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SurfaceCharge.cxx +617 -0
  386. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SurfaceCharge.h +137 -0
  387. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SurfaceComp.cxx +509 -0
  388. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/SurfaceComp.h +70 -0
  389. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/System.cxx +103 -0
  390. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/System.h +89 -0
  391. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Temperature.cxx +423 -0
  392. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Temperature.h +42 -0
  393. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Use.cpp +78 -0
  394. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Use.h +159 -0
  395. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/UserPunch.cpp +32 -0
  396. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/UserPunch.h +39 -0
  397. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/ZedGraph.dll +0 -0
  398. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/advection.cpp +140 -0
  399. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/basicsubs.cpp +4333 -0
  400. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cl1.cpp +881 -0
  401. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/PHRQ_base.cxx +117 -0
  402. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/PHRQ_base.h +48 -0
  403. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/PHRQ_exports.h +20 -0
  404. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/PHRQ_io.cpp +914 -0
  405. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/PHRQ_io.h +207 -0
  406. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/Parser.cxx +1331 -0
  407. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/Parser.h +310 -0
  408. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/Utils.cxx +263 -0
  409. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/Utils.h +29 -0
  410. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/phrqtype.h +18 -0
  411. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cvdense.cpp +566 -0
  412. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cvdense.h +267 -0
  413. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cvode.cpp +3939 -0
  414. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cvode.h +940 -0
  415. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cxxKinetics.cxx +617 -0
  416. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cxxKinetics.h +78 -0
  417. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cxxMix.cxx +154 -0
  418. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/cxxMix.h +58 -0
  419. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/dense.cpp +175 -0
  420. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/dense.h +341 -0
  421. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/dumper.cpp +277 -0
  422. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/dumper.h +60 -0
  423. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/gases.cpp +748 -0
  424. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/global_structures.h +1672 -0
  425. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/input.cpp +133 -0
  426. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/integrate.cpp +1219 -0
  427. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/inverse.cpp +5135 -0
  428. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/isotopes.cpp +1813 -0
  429. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/kinetics.cpp +3180 -0
  430. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/mainsubs.cpp +2320 -0
  431. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/model.cpp +5843 -0
  432. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/nvector.cpp +272 -0
  433. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/nvector.h +485 -0
  434. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/nvector_serial.cpp +1032 -0
  435. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/nvector_serial.h +369 -0
  436. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/parse.cpp +1044 -0
  437. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/phqalloc.cpp +316 -0
  438. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/phqalloc.h +47 -0
  439. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/pitzer.cpp +2709 -0
  440. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/pitzer_structures.cpp +225 -0
  441. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/prep.cpp +6267 -0
  442. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/print.cpp +3673 -0
  443. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/read.cpp +10245 -0
  444. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/readtr.cpp +1495 -0
  445. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/runner.cpp +158 -0
  446. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/runner.h +33 -0
  447. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/sit.cpp +1684 -0
  448. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/smalldense.cpp +324 -0
  449. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/smalldense.h +261 -0
  450. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/spread.cpp +1309 -0
  451. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/step.cpp +1566 -0
  452. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/structures.cpp +3381 -0
  453. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/sundialsmath.cpp +133 -0
  454. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/sundialsmath.h +162 -0
  455. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/sundialstypes.h +183 -0
  456. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/tally.cpp +1288 -0
  457. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/tidy.cpp +5600 -0
  458. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/transport.cpp +6403 -0
  459. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/utilities.cpp +1339 -0
  460. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/thread.h +64 -0
  461. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/CMakeLists.txt +133 -0
  462. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/Makefile.am +45 -0
  463. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/Makefile.in +1128 -0
  464. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/ex2.in +26 -0
  465. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/main.f90 +31 -0
  466. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/main77.f +6 -0
  467. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/main_fortran.cxx +8 -0
  468. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/phreeqc.dat.in +1556 -0
  469. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/test_c.c +148 -0
  470. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/test_cxx.cxx +152 -0
  471. pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/tests/test_f90.F90 +328 -0
  472. pyEQL/phreeqc/iphreeqc_wrapper.cpp +75 -0
  473. pyEQL/phreeqc/solution.py +74 -0
  474. pyEQL/phreeqc/var.py +50 -0
  475. pyEQL/presets/Ringers lactate.yaml +20 -0
  476. pyEQL/presets/__init__.py +17 -0
  477. pyEQL/presets/normal saline.yaml +17 -0
  478. pyEQL/presets/rainwater.yaml +17 -0
  479. pyEQL/presets/seawater.yaml +29 -0
  480. pyEQL/presets/urine.yaml +26 -0
  481. pyEQL/presets/wastewater.yaml +21 -0
  482. pyEQL/py.typed +0 -0
  483. pyEQL/salt_ion_match.py +112 -0
  484. pyEQL/solute.py +163 -0
  485. pyEQL/solution.py +2714 -0
  486. pyEQL/utils.py +237 -0
  487. pyeql-1.4.0rc9.dist-info/METADATA +130 -0
  488. pyeql-1.4.0rc9.dist-info/RECORD +491 -0
  489. pyeql-1.4.0rc9.dist-info/WHEEL +6 -0
  490. pyeql-1.4.0rc9.dist-info/licenses/AUTHORS.md +21 -0
  491. pyeql-1.4.0rc9.dist-info/licenses/LICENSE.txt +20 -0
@@ -0,0 +1,137 @@
1
+ #if !defined(SURFACECHARGE_H_INCLUDED)
2
+ #define SURFACECHARGE_H_INCLUDED
3
+
4
+ #include <cassert> // assert
5
+ #include <map> // std::map
6
+ #include <string> // std::string
7
+ #include <list> // std::list
8
+ #include <vector> // std::vector
9
+
10
+ #include "NameDouble.h"
11
+ #include "PHRQ_base.h"
12
+ class cxxSpeciesDL
13
+ {
14
+ public:
15
+ cxxSpeciesDL()
16
+ {
17
+ g_moles = dg_g_moles = dx_moles = dh2o_moles = drelated_moles = 0;
18
+ }
19
+ LDBLE Get_g_moles(void) const {return g_moles;}
20
+ void Set_g_moles(LDBLE t) {g_moles = t;}
21
+ LDBLE Get_dg_g_moles(void) const {return dg_g_moles;}
22
+ void Set_dg_g_moles(LDBLE t) {dg_g_moles = t;}
23
+ LDBLE Get_dx_moles(void) const {return dx_moles;}
24
+ void Set_dx_moles(LDBLE t) {dx_moles = t;}
25
+ LDBLE Get_dh2o_moles(void) const {return dh2o_moles;}
26
+ void Set_dh2o_moles(LDBLE t) {dh2o_moles = t;}
27
+ LDBLE Get_drelated_moles(void) const {return drelated_moles;}
28
+ void Set_drelated_moles(LDBLE t) {drelated_moles = t;}
29
+
30
+ LDBLE *Get_g_moles_address(void) {return &g_moles;}
31
+ LDBLE *Get_dg_g_moles_address(void) {return &dg_g_moles;}
32
+ LDBLE *Get_dx_moles_address(void) {return &dx_moles;}
33
+ LDBLE *Get_dh2o_moles_address(void) {return &dh2o_moles;}
34
+ LDBLE *Get_drelated_moles_address(void) {return &drelated_moles;}
35
+
36
+ protected:
37
+ LDBLE g_moles;
38
+ LDBLE dg_g_moles; /* g_moles*dgterm */
39
+ LDBLE dx_moles;
40
+ LDBLE dh2o_moles; /* moles*g*Ws/Waq */
41
+ LDBLE drelated_moles; /* for related phase */
42
+ };
43
+ class cxxSurfDL
44
+ {
45
+ public:
46
+ cxxSurfDL()
47
+ {
48
+ g = dg = psi_to_z = 0;
49
+ }
50
+ LDBLE Get_g(void) const {return g;}
51
+ void Set_g(LDBLE t) {g = t;}
52
+ LDBLE Get_dg(void) const {return dg;}
53
+ void Set_dg(LDBLE t) {dg = t;}
54
+ LDBLE Get_psi_to_z(void) const {return psi_to_z;}
55
+ void Set_psi_to_z(LDBLE t) {psi_to_z = t;}
56
+ void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
57
+ void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
58
+
59
+ protected:
60
+ LDBLE g;
61
+ LDBLE dg;
62
+ LDBLE psi_to_z;
63
+ };
64
+ class cxxSurfaceCharge: public PHRQ_base
65
+ {
66
+
67
+ public:
68
+
69
+ cxxSurfaceCharge(PHRQ_io *io=NULL);
70
+ cxxSurfaceCharge(struct surface_charge *, PHRQ_io *io=NULL);
71
+ virtual ~cxxSurfaceCharge();
72
+
73
+ class master *Get_psi_master();
74
+ void dump_xml(std::ostream & os, unsigned int indent = 0) const;
75
+ void dump_raw(std::ostream & s_oss, unsigned int indent) const;
76
+ void read_raw(CParser & parser, bool check = true);
77
+ void add(const cxxSurfaceCharge & comp, LDBLE extensive);
78
+ void multiply(LDBLE extensive);
79
+
80
+ const std::string &Get_name() const {return this->name;}
81
+ void Set_name(const char * f) {this->name = f ? f : "";}
82
+ LDBLE Get_specific_area() const {return this->specific_area;}
83
+ void Set_specific_area(LDBLE d) {this->specific_area = d;}
84
+ LDBLE Get_grams() const {return this->grams;}
85
+ void Set_grams(LDBLE d) {this->grams = d;}
86
+ LDBLE Get_charge_balance() const {return this->charge_balance;}
87
+ void Set_charge_balance(LDBLE d) {this->charge_balance = d;}
88
+ LDBLE Get_mass_water() const {return this->mass_water;}
89
+ void Set_mass_water(LDBLE d) {this->mass_water = d;}
90
+ LDBLE Get_DDL_viscosity(void) const { return DDL_viscosity; }
91
+ void Set_DDL_viscosity(LDBLE t) { DDL_viscosity = t; }
92
+ LDBLE Get_f_free() const {return this->f_free;}
93
+ void Set_f_free(LDBLE d) {this->f_free = d;}
94
+ LDBLE Get_la_psi() const {return this->la_psi;}
95
+ void Set_la_psi(LDBLE d) {this->la_psi = d;}
96
+ LDBLE Get_capacitance0() const {return this->capacitance[0];}
97
+ void Set_capacitance0(LDBLE d) {this->capacitance[0] = d;}
98
+ LDBLE Get_capacitance1() const {return this->capacitance[1];}
99
+ void Set_capacitance1(LDBLE d) {this->capacitance[1] = d;}
100
+ LDBLE Get_sigma0() const {return this->sigma0;}
101
+ void Set_sigma0(LDBLE d) {this->sigma0 = d;}
102
+ LDBLE Get_sigma1() const {return this->sigma1;}
103
+ void Set_sigma1(LDBLE d) {this->sigma1 = d;}
104
+ LDBLE Get_sigma2() const {return this->sigma2;}
105
+ void Set_sigma2(LDBLE d) {this->sigma2 = d;}
106
+ LDBLE Get_sigmaddl() const {return this->sigmaddl;}
107
+ void Set_sigmaddl(LDBLE d) {this->sigmaddl = d;}
108
+ cxxNameDouble & Get_diffuse_layer_totals(void) { return this->diffuse_layer_totals; }
109
+ const cxxNameDouble & Get_diffuse_layer_totals(void)const { return this->diffuse_layer_totals; }
110
+ void Set_diffuse_layer_totals(cxxNameDouble & nd) {this->diffuse_layer_totals = nd;}
111
+ std::map<LDBLE, cxxSurfDL> &Get_g_map(void) {return g_map;}
112
+ void Set_g_map(std::map<LDBLE, cxxSurfDL> & t) {g_map = t;}
113
+ std::map<LDBLE, LDBLE> &Get_z_gMCD_map(void) { return z_gMCD_map; } // z, exp(-zF Psi / RT) * fraction of dl water
114
+ std::map<int, double> & Get_dl_species_map(void) {return this->dl_species_map;}
115
+ void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
116
+ void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
117
+
118
+ protected:
119
+ std::string name;
120
+ LDBLE specific_area;
121
+ LDBLE grams;
122
+ LDBLE charge_balance;
123
+ LDBLE mass_water;
124
+ LDBLE DDL_viscosity;
125
+ LDBLE f_free;
126
+ LDBLE la_psi;
127
+ LDBLE capacitance[2];
128
+ cxxNameDouble diffuse_layer_totals;
129
+ // workspace variables
130
+ LDBLE sigma0, sigma1, sigma2, sigmaddl;
131
+ std::map<LDBLE, cxxSurfDL> g_map;
132
+ std::map<LDBLE, LDBLE> z_gMCD_map;
133
+ const static std::vector < std::string > vopts;
134
+ std::map<int, double> dl_species_map;
135
+ };
136
+
137
+ #endif // !defined(SURFACECHARGE_H_INCLUDED)
@@ -0,0 +1,509 @@
1
+ // SurfaceComp.cxx: implementation of the cxxSurfaceComp class.
2
+ //
3
+ //////////////////////////////////////////////////////////////////////
4
+ #ifdef _DEBUG
5
+ #pragma warning(disable : 4786) // disable truncation warning (Only used by debugger)
6
+ #endif
7
+ #include <cassert> // assert
8
+ #include <algorithm> // std::sort
9
+
10
+ #include "Utils.h" // define first
11
+ #include "Phreeqc.h"
12
+ #include "SurfaceComp.h"
13
+ #include "phqalloc.h"
14
+ #include "Dictionary.h"
15
+
16
+ #if defined(PHREEQCI_GUI)
17
+ #ifdef _DEBUG
18
+ #define new DEBUG_NEW
19
+ #undef THIS_FILE
20
+ static char THIS_FILE[] = __FILE__;
21
+ #endif
22
+ #endif
23
+
24
+ //////////////////////////////////////////////////////////////////////
25
+ // Construction/Destruction
26
+ //////////////////////////////////////////////////////////////////////
27
+
28
+ cxxSurfaceComp::cxxSurfaceComp(PHRQ_io *io)
29
+ :
30
+ PHRQ_base(io)
31
+ //
32
+ // default constructor for cxxSurfaceComp
33
+ //
34
+ {
35
+ formula_z = 0.0;
36
+ moles = 0.0;
37
+ totals.type = cxxNameDouble::ND_ELT_MOLES;
38
+ la = 0.0;
39
+ charge_balance = 0;
40
+ phase_proportion = 0.0;
41
+ Dw = 0.0;
42
+ }
43
+ cxxSurfaceComp::~cxxSurfaceComp()
44
+ {
45
+ }
46
+
47
+ void
48
+ cxxSurfaceComp::dump_xml(std::ostream & s_oss, unsigned int indent) const
49
+ {
50
+ unsigned int i;
51
+ s_oss.precision(DBL_DIG - 1);
52
+ std::string indent0(""), indent1(""), indent2("");
53
+ for (i = 0; i < indent; ++i)
54
+ indent0.append(Utilities::INDENT);
55
+ for (i = 0; i < indent + 1; ++i)
56
+ indent1.append(Utilities::INDENT);
57
+ for (i = 0; i < indent + 2; ++i)
58
+ indent2.append(Utilities::INDENT);
59
+
60
+ // Surf_Comp element and attributes
61
+
62
+ //s_oss << indent0 << "formula=\"" << this->formula << "\"" << "\n";
63
+ s_oss << indent0 << "formula_z=\"" << this->formula_z << "\"" << "\n";
64
+ s_oss << indent0 << "moles=\"" << this->moles << "\"" << "\n";
65
+ s_oss << indent0 << "la=\"" << this->la << "\"" << "\n";
66
+ s_oss << indent0 << "charge_balance=\"" << this->charge_balance << "\"" << "\n";
67
+ s_oss << indent0 << "phase_proportion=\"" << this->phase_proportion << "\"" << "\n";
68
+ s_oss << indent0 << "Dw=\"" << this->Dw << "\"" << "\n";
69
+ s_oss << indent0 << "charge_name=\"" << this->charge_name << "\"" << "\n";
70
+ if (this->phase_name.size() != 0)
71
+ {
72
+ s_oss << indent0 << "phase_name=\"" << this->phase_name << "\"" << "\n";
73
+ }
74
+ if (this->rate_name.size() != 0)
75
+ {
76
+ s_oss << indent0 << "rate_name=\"" << this->rate_name << "\"" << "\n";
77
+ }
78
+
79
+ // totals
80
+ s_oss << indent0;
81
+ s_oss << "<totals " << "\n";
82
+ this->totals.dump_xml(s_oss, indent + 1);
83
+ }
84
+
85
+ void
86
+ cxxSurfaceComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
87
+ {
88
+ unsigned int i;
89
+ s_oss.precision(DBL_DIG - 1);
90
+ std::string indent0(""), indent1(""), indent2("");
91
+ for (i = 0; i < indent; ++i)
92
+ indent0.append(Utilities::INDENT);
93
+ for (i = 0; i < indent + 1; ++i)
94
+ indent1.append(Utilities::INDENT);
95
+ for (i = 0; i < indent + 2; ++i)
96
+ indent2.append(Utilities::INDENT);
97
+
98
+ s_oss << indent0 << "# SURFACE_MODIFY candidate identifiers #\n";
99
+ s_oss << indent0 << "-formula_z " << this->formula_z << "\n";
100
+ s_oss << indent0 << "-moles " << this->moles << "\n";
101
+ s_oss << indent0 << "-la " << this->la << "\n";
102
+ s_oss << indent0 << "-charge_balance " << this->charge_balance << "\n";
103
+ if (this->phase_name.size() != 0)
104
+ {
105
+ s_oss << indent0 << "-phase_name " << this->phase_name << "\n";
106
+ }
107
+ if (this->rate_name.size() != 0)
108
+ {
109
+ s_oss << indent0 << "-rate_name " << this->rate_name << "\n";
110
+ }
111
+ s_oss << indent0 << "-phase_proportion " << this->phase_proportion << "\n";
112
+ s_oss << indent0 << "-Dw " << this->Dw << "\n";
113
+ s_oss << indent0 << "-charge_name " << this->charge_name << "\n";
114
+ s_oss << indent0 << "-master_element " << this->master_element << "\n";
115
+ // totals
116
+ s_oss << indent0;
117
+ s_oss << "-totals" << "\n";
118
+ this->totals.dump_raw(s_oss, indent + 1);
119
+ }
120
+
121
+ void
122
+ cxxSurfaceComp::read_raw(CParser & parser, bool check)
123
+ {
124
+ std::string str;
125
+
126
+
127
+ std::istream::pos_type ptr;
128
+ std::istream::pos_type next_char;
129
+ std::string token;
130
+ int opt_save;
131
+
132
+ opt_save = CParser::OPT_ERROR;
133
+
134
+ bool master_element_defined(false);
135
+ bool charge_name_defined(false);
136
+ bool moles_defined(false);
137
+ bool la_defined(false);
138
+ bool charge_balance_defined(false);
139
+ bool formula_z_defined(false);
140
+ bool Dw_defined(false);
141
+ bool totals_defined(false);
142
+
143
+ for (;;)
144
+ {
145
+ int opt = parser.get_option(vopts, next_char);
146
+ if (opt == CParser::OPT_DEFAULT)
147
+ {
148
+ opt = opt_save;
149
+ }
150
+
151
+ switch (opt)
152
+ {
153
+ case CParser::OPT_EOF:
154
+ break;
155
+ case CParser::OPT_KEYWORD:
156
+ break;
157
+ case CParser::OPT_DEFAULT:
158
+ case CParser::OPT_ERROR:
159
+ opt = CParser::OPT_KEYWORD;
160
+ // Allow return to Surface for more processing
161
+ break;
162
+
163
+ case 0: // formula
164
+ output_msg("-formula is obsolete in surface comp raw");
165
+ break;
166
+
167
+ case 1: // moles
168
+ if (!(parser.get_iss() >> this->moles))
169
+ {
170
+ this->moles = 0;
171
+ parser.incr_input_error();
172
+ parser.error_msg("Expected numeric value for moles.",
173
+ PHRQ_io::OT_CONTINUE);
174
+ }
175
+ moles_defined = true;
176
+ break;
177
+
178
+ case 2: // la
179
+ if (!(parser.get_iss() >> this->la))
180
+ {
181
+ this->la = 0;
182
+ parser.incr_input_error();
183
+ parser.error_msg("Expected numeric value for la.",
184
+ PHRQ_io::OT_CONTINUE);
185
+ }
186
+ la_defined = true;
187
+ break;
188
+ case 3: // charge_number not used
189
+ parser.warning_msg("-charge_number identifier is obsolete.");
190
+ break;
191
+
192
+ case 4: // charge_balance
193
+ if (!(parser.get_iss() >> this->charge_balance))
194
+ {
195
+ this->charge_balance = 0;
196
+ parser.incr_input_error();
197
+ parser.error_msg("Expected numeric value for charge_balance.",
198
+ PHRQ_io::OT_CONTINUE);
199
+ }
200
+ charge_balance_defined = true;
201
+ break;
202
+
203
+ case 5: // phase_name
204
+ if (!(parser.get_iss() >> str))
205
+ {
206
+ this->phase_name.clear();
207
+ parser.incr_input_error();
208
+ parser.error_msg("Expected string value for phase_name.",
209
+ PHRQ_io::OT_CONTINUE);
210
+ }
211
+ else
212
+ {
213
+ this->phase_name = str;
214
+ }
215
+ break;
216
+
217
+ case 6: // rate_name
218
+ if (!(parser.get_iss() >> str))
219
+ {
220
+ this->rate_name.clear();
221
+ parser.incr_input_error();
222
+ parser.error_msg("Expected string value for rate_name.",
223
+ PHRQ_io::OT_CONTINUE);
224
+ }
225
+ else
226
+ {
227
+ this->rate_name = str;
228
+ }
229
+ break;
230
+
231
+ case 7: // phase_proportion
232
+ if (!(parser.get_iss() >> this->phase_proportion))
233
+ {
234
+ this->phase_proportion = 0;
235
+ parser.incr_input_error();
236
+ parser.
237
+ error_msg("Expected numeric value for phase_proportion.",
238
+ PHRQ_io::OT_CONTINUE);
239
+ }
240
+ break;
241
+
242
+ case 8: // totals
243
+ if (this->totals.read_raw(parser, next_char) !=
244
+ CParser::PARSER_OK)
245
+ {
246
+ parser.incr_input_error();
247
+ parser.
248
+ error_msg
249
+ ("Expected element name and molality for SurfaceComp totals.",
250
+ PHRQ_io::OT_CONTINUE);
251
+ }
252
+ totals_defined = true;
253
+ opt_save = 8;
254
+ break;
255
+
256
+ case 9: // formula_z
257
+ if (!(parser.get_iss() >> this->formula_z))
258
+ {
259
+ this->formula_z = 0;
260
+ parser.incr_input_error();
261
+ parser.error_msg("Expected numeric value for formula_z.",
262
+ PHRQ_io::OT_CONTINUE);
263
+ }
264
+ formula_z_defined = true;
265
+ break;
266
+
267
+ case 10: // formula_totals
268
+ parser.warning_msg("-formula_totals is an obsolete identifier.");
269
+ break;
270
+
271
+ case 11: // Dw
272
+ if (!(parser.get_iss() >> this->Dw))
273
+ {
274
+ this->Dw = 0.0;
275
+ parser.incr_input_error();
276
+ parser.error_msg("Expected numeric value for Dw.",
277
+ PHRQ_io::OT_CONTINUE);
278
+ }
279
+ Dw_defined = true;
280
+ break;
281
+ case 12: // charge_name
282
+ if (!(parser.get_iss() >> str))
283
+ {
284
+ this->charge_name.clear();
285
+ parser.incr_input_error();
286
+ parser.error_msg("Expected string value for charge_name.",
287
+ PHRQ_io::OT_CONTINUE);
288
+ }
289
+ else
290
+ {
291
+ this->charge_name = str;
292
+ }
293
+ charge_name_defined = true;
294
+ break;
295
+ case 13: // master_element
296
+ if (!(parser.get_iss() >> str))
297
+ {
298
+ this->master_element.clear();
299
+ parser.incr_input_error();
300
+ parser.error_msg("Expected string value for master_element.",
301
+ PHRQ_io::OT_CONTINUE);
302
+ }
303
+ else
304
+ {
305
+ this->master_element = str;
306
+ }
307
+ master_element_defined = true;
308
+ break;
309
+ }
310
+ if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
311
+ break;
312
+ }
313
+ if (check)
314
+ {
315
+ // members that must be defined
316
+ if (charge_name_defined == false)
317
+ {
318
+ parser.incr_input_error();
319
+ parser.error_msg("Charge_name not defined for SurfaceComp input.",
320
+ PHRQ_io::OT_CONTINUE);
321
+ }
322
+ if (formula_z_defined == false)
323
+ {
324
+ parser.incr_input_error();
325
+ parser.error_msg("Formula_z not defined for ExchComp input.",
326
+ PHRQ_io::OT_CONTINUE);
327
+ }
328
+ if (moles_defined == false)
329
+ {
330
+ parser.incr_input_error();
331
+ parser.error_msg("Moles not defined for SurfaceComp input.",
332
+ PHRQ_io::OT_CONTINUE);
333
+ }
334
+ if (la_defined == false)
335
+ {
336
+ parser.incr_input_error();
337
+ parser.error_msg("La not defined for SurfaceComp input.",
338
+ PHRQ_io::OT_CONTINUE);
339
+ }
340
+
341
+ if (charge_balance_defined == false)
342
+ {
343
+ parser.incr_input_error();
344
+ parser.error_msg("Charge_balance not defined for SurfaceComp input.",
345
+ PHRQ_io::OT_CONTINUE);
346
+ }
347
+ if (Dw_defined == false)
348
+ {
349
+ parser.incr_input_error();
350
+ parser.error_msg("Dw not defined for SurfaceComp input.",
351
+ PHRQ_io::OT_CONTINUE);
352
+ }
353
+ if (master_element_defined == false)
354
+ {
355
+ parser.incr_input_error();
356
+ parser.error_msg("Master_element name not defined for SurfaceComp input.",
357
+ PHRQ_io::OT_CONTINUE);
358
+ }
359
+ if (totals_defined == false)
360
+ {
361
+ parser.incr_input_error();
362
+ parser.error_msg("Totals not defined for SurfaceComp input.",
363
+ PHRQ_io::OT_CONTINUE);
364
+ }
365
+ }
366
+ }
367
+
368
+ void
369
+ cxxSurfaceComp::add(const cxxSurfaceComp & addee, LDBLE extensive)
370
+ {
371
+ if (extensive == 0.0)
372
+ return;
373
+ if (addee.formula.size() == 0)
374
+ return;
375
+
376
+ if (this->formula.size() == 0 && addee.formula.size() == 0)
377
+ {
378
+ return;
379
+ }
380
+ assert(this->formula == addee.formula);
381
+ assert(this->formula_z == addee.formula_z);
382
+ if (this->formula.size() == 0 && addee.formula.size() != 0)
383
+ {
384
+ this->formula = addee.formula;
385
+ }
386
+
387
+ // this and addee must have same formula
388
+ // otherwise generate a new exchcomp with multiply
389
+ LDBLE ext1, ext2, f1, f2;
390
+ ext1 = this->moles;
391
+ ext2 = addee.moles * extensive;
392
+ if (ext1 + ext2 != 0)
393
+ {
394
+ f1 = ext1 / (ext1 + ext2);
395
+ f2 = ext2 / (ext1 + ext2);
396
+ }
397
+ else
398
+ {
399
+ f1 = 0.5;
400
+ f2 = 0.5;
401
+ }
402
+ this->moles += addee.moles * extensive;
403
+ this->totals.add_extensive(addee.totals, extensive);
404
+ this->la = f1 * this->la + f2 * addee.la;
405
+ this->charge_balance += addee.charge_balance * extensive;
406
+ //if (this->phase_name != addee.phase_name)
407
+ if (Phreeqc::strcmp_nocase(this->phase_name.c_str(),addee.phase_name.c_str()) != 0)
408
+ {
409
+ std::ostringstream oss;
410
+ oss <<
411
+ "Cannot mix two Surface components with same formula and different related phases, "
412
+ << this->formula;
413
+ error_msg(oss.str().c_str(), CONTINUE);
414
+ return;
415
+ }
416
+ else if (this->phase_name.size() != 0)
417
+ {
418
+ this->phase_proportion =
419
+ this->phase_proportion * f1 + addee.phase_proportion * f2;
420
+ }
421
+
422
+ //if (this->rate_name != addee.rate_name)
423
+ if (Phreeqc::strcmp_nocase(this->rate_name.c_str(), addee.rate_name.c_str()) != 0)
424
+ {
425
+ std::ostringstream oss;
426
+ oss <<
427
+ "Cannot mix two surface components with same formula and different related kinetics, "
428
+ << this->formula;
429
+ error_msg(oss.str().c_str(), CONTINUE);
430
+ return;
431
+ }
432
+ else if (this->rate_name.size() != 0)
433
+ {
434
+ //LDBLE phase_proportion;
435
+ this->phase_proportion =
436
+ this->phase_proportion * f1 + addee.phase_proportion * f2;
437
+ }
438
+ if ((this->rate_name.size() != 0 && addee.phase_name.size() != 0) ||
439
+ (this->phase_name.size() != 0 && addee.rate_name.size() != 0))
440
+ {
441
+ std::ostringstream oss;
442
+ oss <<
443
+ "Cannot mix surface components related to phase with surface components related to kinetics, "
444
+ << this->formula;
445
+ error_msg(oss.str().c_str(), CONTINUE);
446
+ return;
447
+ }
448
+
449
+ }
450
+ void
451
+ cxxSurfaceComp::multiply(LDBLE extensive)
452
+ {
453
+ this->moles *= extensive;
454
+
455
+ this->totals.multiply(extensive);
456
+
457
+ this->charge_balance *= extensive;
458
+ }
459
+ void
460
+ cxxSurfaceComp::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
461
+ {
462
+ ints.push_back(dictionary.Find(this->formula));
463
+ doubles.push_back(this->formula_z);
464
+ doubles.push_back(this->moles);
465
+ this->totals.Serialize(dictionary, ints, doubles);
466
+ doubles.push_back(this->la);
467
+ ints.push_back(dictionary.Find(this->charge_name));
468
+ doubles.push_back(this->charge_balance);
469
+ ints.push_back(dictionary.Find(this->phase_name));
470
+ doubles.push_back(this->phase_proportion);
471
+ ints.push_back(dictionary.Find(this->rate_name));
472
+ doubles.push_back(this->Dw);
473
+ ints.push_back(dictionary.Find(this->master_element));
474
+ }
475
+
476
+ void
477
+ cxxSurfaceComp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd)
478
+ {
479
+ this->formula = dictionary.GetWords()[ints[ii++]];
480
+ this->formula_z = doubles[dd++];
481
+ this->moles = doubles[dd++];
482
+ this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
483
+ this->la = doubles[dd++];
484
+ this->charge_name = dictionary.GetWords()[ints[ii++]];
485
+ this->charge_balance = doubles[dd++];
486
+ this->phase_name = dictionary.GetWords()[ints[ii++]];
487
+ this->phase_proportion = doubles[dd++];
488
+ this->rate_name = dictionary.GetWords()[ints[ii++]];
489
+ this->Dw = doubles[dd++];
490
+ this->master_element = dictionary.GetWords()[ints[ii++]];
491
+ }
492
+
493
+ const std::vector< std::string >::value_type temp_vopts[] = {
494
+ std::vector< std::string >::value_type("formula"), // 0
495
+ std::vector< std::string >::value_type("moles"), // 1
496
+ std::vector< std::string >::value_type("la"), // 2
497
+ std::vector< std::string >::value_type("charge_number"), // 3
498
+ std::vector< std::string >::value_type("charge_balance"), // 4
499
+ std::vector< std::string >::value_type("phase_name"), // 5
500
+ std::vector< std::string >::value_type("rate_name"), // 6
501
+ std::vector< std::string >::value_type("phase_proportion"), // 7
502
+ std::vector< std::string >::value_type("totals"), // 8
503
+ std::vector< std::string >::value_type("formula_z"), // 9
504
+ std::vector< std::string >::value_type("formula_totals"), // 10
505
+ std::vector< std::string >::value_type("dw"), // 11
506
+ std::vector< std::string >::value_type("charge_name"), // 12
507
+ std::vector< std::string >::value_type("master_element") // 13
508
+ };
509
+ const std::vector< std::string > cxxSurfaceComp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);