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MinimalGeochemicalSystemTest.C
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1//* This file is part of the MOOSE framework
2//* https://mooseframework.inl.gov
3//*
4//* All rights reserved, see COPYRIGHT for full restrictions
5//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
6//*
7//* Licensed under LGPL 2.1, please see LICENSE for details
8//* https://www.gnu.org/licenses/lgpl-2.1.html
9
10#include "gtest/gtest.h"
11
12#include "PertinentGeochemicalSystem.h"
13
14const Real eps = 1E-12; // accounts for precision loss when substituting reactions
15
23TEST(PertinentGeochemicalSystemTest, basisExceptions)
24{
25 GeochemicalDatabaseReader database("database/moose_testdb.json");
26
27 try
28 {
29 PertinentGeochemicalSystem model(
30 database, {"H2O", "Ca++", "(O-phth)--", "H2O", "Na+"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
31 FAIL() << "Missing expected exception.";
32 }
33 catch (const std::exception & e)
34 {
35 std::string msg(e.what());
36 ASSERT_TRUE(msg.find("H2O exists more than once in the basis species list") !=
37 std::string::npos)
38 << "Failed with unexpected error message: " << msg;
39 }
40
41 try
42 {
43 PertinentGeochemicalSystem model(database,
44 {"Ca++", "H2O", "H+", "(O-phth)--", "Am++++"},
45 {},
46 {},
47 {},
48 {},
49 {},
50 "O2(aq)",
51 "e-");
52 FAIL() << "Missing expected exception.";
53 }
54 catch (const std::exception & e)
55 {
56 std::string msg(e.what());
57 ASSERT_TRUE(msg.find("First member of basis species list must be H2O") != std::string::npos)
58 << "Failed with unexpected error message: " << msg;
59 }
60
61 try
62 {
63 PertinentGeochemicalSystem model(
64 database,
65 {"H2O", "Ca++", "H+", "(O-phth)--", "Am++++", "does_not_exist"},
66 {},
67 {},
68 {},
69 {},
70 {},
71 "O2(aq)",
72 "e-");
73 FAIL() << "Missing expected exception.";
74 }
75 catch (const std::exception & e)
76 {
77 std::string msg(e.what());
78 ASSERT_TRUE(msg.find("does_not_exist does not exist in the basis species or redox species in "
79 "database/moose_testdb.json") != std::string::npos)
80 << "Failed with unexpected error message: " << msg;
81 }
82}
83
93TEST(PertinentGeochemicalSystemTest, mineralExceptions)
94{
95 GeochemicalDatabaseReader database("database/moose_testdb.json");
96
97 try
98 {
99 PertinentGeochemicalSystem model(database,
100 {"H2O", "Ca++", "H+", "(O-phth)--", "HCO3-"},
101 {"Calcite", "Calcite_asdf", "Calcite"},
102 {},
103 {},
104 {},
105 {},
106 "O2(aq)",
107 "e-");
108 FAIL() << "Missing expected exception.";
109 }
110 catch (const std::exception & e)
111 {
112 std::string msg(e.what());
113 ASSERT_TRUE(msg.find("Calcite exists more than once in the minerals list") != std::string::npos)
114 << "Failed with unexpected error message: " << msg;
115 }
116
117 try
118 {
119 PertinentGeochemicalSystem model(database,
120 {"H2O", "Ca++", "H+", "Am++++", "HCO3-"},
121 {"Calcite", "Calcite_asdf", "does_not_exist"},
122 {},
123 {},
124 {},
125 {},
126 "O2(aq)",
127 "e-");
128 FAIL() << "Missing expected exception.";
129 }
130 catch (const std::exception & e)
131 {
132 std::string msg(e.what());
133 ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
134 std::string::npos)
135 << "Failed with unexpected error message: " << msg;
136 }
137
138 try
139 {
140 PertinentGeochemicalSystem model(database,
141 {"H2O", "H+", "(O-phth)--", "HCO3-"},
142 {"Calcite"},
143 {},
144 {},
145 {},
146 {},
147 "O2(aq)",
148 "e-");
149 FAIL() << "Missing expected exception.";
150 }
151 catch (const std::exception & e)
152 {
153 std::string msg(e.what());
154 ASSERT_TRUE(msg.find("The reaction for Calcite depends on Ca++ which is not reducable to a set "
155 "of basis species") != std::string::npos)
156 << "Failed with unexpected error message: " << msg;
157 }
158
159 try
160 {
161 PertinentGeochemicalSystem model(
162 database, {"H2O", "H+", "O2(aq)"}, {"Fe(OH)3(ppd)"}, {}, {}, {}, {}, "O2(aq)", "e-");
163 FAIL() << "Missing expected exception.";
164 }
165 catch (const std::exception & e)
166 {
167 std::string msg(e.what());
168 ASSERT_TRUE(msg.find("The reaction for Fe(OH)3(ppd) depends on Fe+++ which is not reducable to "
169 "a set of basis species") != std::string::npos)
170 << "Failed with unexpected error message: " << msg;
171 }
172
173 try
174 {
175 PertinentGeochemicalSystem model(database,
176 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH"},
177 {"Fe(OH)3(ppd)"},
178 {},
179 {},
180 {},
181 {},
182 "O2(aq)",
183 "e-");
184 FAIL() << "Missing expected exception.";
185 }
186 catch (const std::exception & e)
187 {
188 std::string msg(e.what());
189 ASSERT_TRUE(msg.find("The sorbing sites for Fe(OH)3(ppd) include >(w)FeOH which is not in the "
190 "basis_species list") != std::string::npos)
191 << "Failed with unexpected error message: " << msg;
192 }
193
194 // This should pass since the basis species can make Fe+++, which then makes Fe(OH)3(ppd), and the
195 // surface sites for Fe(OH)3(ppd) are included
196 PertinentGeochemicalSystem model(database,
197 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH", ">(w)FeOH"},
198 {"Fe(OH)3(ppd)"},
199 {},
200 {},
201 {},
202 {},
203 "O2(aq)",
204 "e-");
205}
206
214TEST(PertinentGeochemicalSystemTest, gasExceptions)
215{
216 GeochemicalDatabaseReader database("database/moose_testdb.json");
217
218 try
219 {
220 PertinentGeochemicalSystem model(database,
221 {"H2O", "Ca++", "H+", "HCO3-", "CH4(aq)"},
222 {"Calcite"},
223 {"CH4(g)", "CH4(g)"},
224 {},
225 {},
226 {},
227 "O2(aq)",
228 "e-");
229 FAIL() << "Missing expected exception.";
230 }
231 catch (const std::exception & e)
232 {
233 std::string msg(e.what());
234 ASSERT_TRUE(msg.find("CH4(g) exists more than once in the gases list") != std::string::npos)
235 << "Failed with unexpected error message: " << msg;
236 }
237
238 try
239 {
240 PertinentGeochemicalSystem model(database,
241 {"H2O", "Ca++", "H+", "HCO3-", "CH4(aq)"},
242 {"Calcite"},
243 {"CH4(g)", "does_not_exist"},
244 {},
245 {},
246 {},
247 "O2(aq)",
248 "e-");
249 FAIL() << "Missing expected exception.";
250 }
251 catch (const std::exception & e)
252 {
253 std::string msg(e.what());
254 ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
255 std::string::npos)
256 << "Failed with unexpected error message: " << msg;
257 }
258
259 try
260 {
261 PertinentGeochemicalSystem model(database,
262 {"H2O", "Ca++", "H+", "HCO3-"},
263 {"Calcite"},
264 {"CH4(g)"},
265 {},
266 {},
267 {},
268 "O2(aq)",
269 "e-");
270 FAIL() << "Missing expected exception.";
271 }
272 catch (const std::exception & e)
273 {
274 std::string msg(e.what());
275 ASSERT_TRUE(msg.find("The reaction for CH4(g) depends on CH4(aq) which is not reducable to a "
276 "set of basis species") != std::string::npos)
277 << "Failed with unexpected error message: " << msg;
278 }
279
280 // this should pass: CH4(g) depends on the redox couple CH4(aq) which in turn depends on the basis
281 // species provided
282 PertinentGeochemicalSystem model(database,
283 {"H2O", "Ca++", "H+", "HCO3-", "O2(aq)"},
284 {"Calcite"},
285 {"CH4(g)"},
286 {},
287 {},
288 {},
289 "O2(aq)",
290 "e-");
291}
292
303TEST(PertinentGeochemicalSystemTest, kineticMineralExceptions)
304{
305 GeochemicalDatabaseReader database("database/moose_testdb.json");
306
307 try
308 {
309 PertinentGeochemicalSystem model(
310 database, {"H2O"}, {}, {}, {"Calcite", "Calcite_asdf", "Calcite"}, {}, {}, "O2(aq)", "e-");
311 FAIL() << "Missing expected exception.";
312 }
313 catch (const std::exception & e)
314 {
315 std::string msg(e.what());
316 ASSERT_TRUE(msg.find("Calcite exists more than once in the kinetic_minerals list") !=
317 std::string::npos)
318 << "Failed with unexpected error message: " << msg;
319 }
320
321 try
322 {
323 PertinentGeochemicalSystem model(database,
324 {"H2O", "Ca++", "HCO3-", "H+"},
325 {"Calcite_asdf"},
326 {},
327 {"Calcite", "Calcite_asdf"},
328 {},
329 {},
330 "O2(aq)",
331 "e-");
332 FAIL() << "Missing expected exception.";
333 }
334 catch (const std::exception & e)
335 {
336 std::string msg(e.what());
337 ASSERT_TRUE(msg.find("Calcite_asdf exists in both the minerals and kinetic_minerals lists") !=
338 std::string::npos)
339 << "Failed with unexpected error message: " << msg;
340 }
341
342 try
343 {
344 PertinentGeochemicalSystem model(database,
345 {"H2O", "Ca++", "HCO3-", "H+"},
346 {"Calcite_asdf"},
347 {},
348 {"Calcite", "does_not_exist"},
349 {},
350 {},
351 "O2(aq)",
352 "e-");
353 FAIL() << "Missing expected exception.";
354 }
355 catch (const std::exception & e)
356 {
357 std::string msg(e.what());
358 ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
359 std::string::npos)
360 << "Failed with unexpected error message: " << msg;
361 }
362
363 try
364 {
365 PertinentGeochemicalSystem model(
366 database, {"H2O", "O2(aq)", "H+"}, {}, {}, {"Fe(OH)3(ppd)"}, {}, {}, "O2(aq)", "e-");
367 FAIL() << "Missing expected exception.";
368 }
369 catch (const std::exception & e)
370 {
371 std::string msg(e.what());
372 ASSERT_TRUE(msg.find("The reaction for Fe(OH)3(ppd) depends on Fe+++ which is not reducable to "
373 "a set of basis species") != std::string::npos)
374 << "Failed with unexpected error message: " << msg;
375 }
376
377 try
378 {
379 PertinentGeochemicalSystem model(database,
380 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH"},
381 {},
382 {},
383 {"Fe(OH)3(ppd)"},
384 {},
385 {},
386 "O2(aq)",
387 "e-");
388 FAIL() << "Missing expected exception.";
389 }
390 catch (const std::exception & e)
391 {
392 std::string msg(e.what());
393 ASSERT_TRUE(msg.find("The sorbing sites for Fe(OH)3(ppd) include >(w)FeOH which is not in the "
394 "basis_species list") != std::string::npos)
395 << "Failed with unexpected error message: " << msg;
396 }
397
398 // This should pass since the basis species can make Fe+++, which then makes Fe(OH)3(ppd), and the
399 // surface sites for Fe(OH)3(ppd) are included
400 PertinentGeochemicalSystem model(database,
401 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH", ">(w)FeOH"},
402 {},
403 {},
404 {"Fe(OH)3(ppd)"},
405 {},
406 {},
407 "O2(aq)",
408 "e-");
409}
410
419TEST(PertinentGeochemicalSystemTest, kineticRedoxExceptions)
420{
421 GeochemicalDatabaseReader database("database/moose_testdb.json");
422
423 try
424 {
425 PertinentGeochemicalSystem model(
426 database, {"H2O"}, {}, {}, {}, {"(O-phth)--", "Am++++", "(O-phth)--"}, {}, "O2(aq)", "e-");
427 FAIL() << "Missing expected exception.";
428 }
429 catch (const std::exception & e)
430 {
431 std::string msg(e.what());
432 ASSERT_TRUE(msg.find("(O-phth)-- exists more than once in the kinetic_redox list") !=
433 std::string::npos)
434 << "Failed with unexpected error message: " << msg;
435 }
436
437 try
438 {
439 PertinentGeochemicalSystem model(
440 database, {"H2O", "(O-phth)--"}, {}, {}, {}, {"Am++++", "(O-phth)--"}, {}, "O2(aq)", "e-");
441 FAIL() << "Missing expected exception.";
442 }
443 catch (const std::exception & e)
444 {
445 std::string msg(e.what());
446 ASSERT_TRUE(msg.find("(O-phth)-- exists in both the basis_species and kinetic_redox lists") !=
447 std::string::npos)
448 << "Failed with unexpected error message: " << msg;
449 }
450
451 try
452 {
453 PertinentGeochemicalSystem model(
454 database, {"H2O"}, {}, {}, {}, {"(O-phth)--", "does_not_exist"}, {}, "O2(aq)", "e-");
455 FAIL() << "Missing expected exception.";
456 }
457 catch (const std::exception & e)
458 {
459 std::string msg(e.what());
460 ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
461 std::string::npos)
462 << "Failed with unexpected error message: " << msg;
463 }
464
465 try
466 {
467 PertinentGeochemicalSystem model(
468 database, {"H2O", "HCO3-", "H+"}, {}, {}, {}, {"(O-phth)--"}, {}, "O2(aq)", "e-");
469 FAIL() << "Missing expected exception.";
470 }
471 catch (const std::exception & e)
472 {
473 std::string msg(e.what());
474 ASSERT_TRUE(msg.find("The reaction for (O-phth)-- depends on O2(aq) which is not reducable to "
475 "a set of basis species") != std::string::npos)
476 << "Failed with unexpected error message: " << msg;
477 }
478
479 // this should pass
480 PertinentGeochemicalSystem model(
481 database, {"H2O", "HCO3-", "H+", "O2(aq)"}, {}, {}, {}, {"(O-phth)--"}, {}, "O2(aq)", "e-");
482}
483
491TEST(PertinentGeochemicalSystemTest, kineticSurfaceExceptions)
492{
493 GeochemicalDatabaseReader database("database/moose_testdb.json");
494
495 try
496 {
497 PertinentGeochemicalSystem model(
498 database, {"H2O"}, {}, {}, {}, {}, {">(s)FeO-", ">(s)FeOCa+", ">(s)FeO-"}, "O2(aq)", "e-");
499 FAIL() << "Missing expected exception.";
500 }
501 catch (const std::exception & e)
502 {
503 std::string msg(e.what());
504 ASSERT_TRUE(msg.find(">(s)FeO- exists more than once in the kinetic_surface_species list") !=
505 std::string::npos)
506 << "Failed with unexpected error message: " << msg;
507 }
508
509 try
510 {
511 PertinentGeochemicalSystem model(database,
512 {"H2O"},
513 {},
514 {},
515 {},
516 {},
517 {">(s)FeO-", ">(s)FeOCa+", "does_not_exist"},
518 "O2(aq)",
519 "e-");
520 FAIL() << "Missing expected exception.";
521 }
522 catch (const std::exception & e)
523 {
524 std::string msg(e.what());
525 ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
526 std::string::npos)
527 << "Failed with unexpected error message: " << msg;
528 }
529
530 try
531 {
532 PertinentGeochemicalSystem model(
533 database, {"H2O", "H+"}, {}, {}, {}, {}, {">(s)FeO-"}, "O2(aq)", "e-");
534 FAIL() << "Missing expected exception.";
535 }
536 catch (const std::exception & e)
537 {
538 std::string msg(e.what());
539 ASSERT_TRUE(msg.find("The reaction for >(s)FeO- depends on >(s)FeOH which is not reducable to "
540 "a set of basis species") != std::string::npos)
541 << "Failed with unexpected error message: " << msg;
542 }
543
544 // this should pass
545 PertinentGeochemicalSystem model(
546 database, {"H2O", "H+", ">(s)FeOH"}, {}, {}, {}, {}, {">(s)FeO-"}, "O2(aq)", "e-");
547}
548
550TEST(PertinentGeochemicalSystemTest, temperatures)
551{
552 GeochemicalDatabaseReader database("database/moose_testdb.json");
553
554 PertinentGeochemicalSystem model(database, {"H2O"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
555 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
556
557 ASSERT_EQ(mgd.original_database->getTemperatures(), database.getTemperatures());
558}
559
565TEST(PertinentGeochemicalSystemTest, names1)
566{
567 GeochemicalDatabaseReader database("database/moose_testdb.json");
568
569 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
570 // >(s)FeO-
571 PertinentGeochemicalSystem model(database,
572 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
573 {"Calcite"},
574 {"O2(g)"},
575 {"Calcite_asdf"},
576 {"CH4(aq)"},
577 {">(s)FeOCa+"},
578 "O2(aq)",
579 "e-");
580 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
581
582 ASSERT_EQ(mgd.basis_species_index.size(), (std::size_t)6);
583 for (const auto & sp : mgd.basis_species_index)
584 ASSERT_EQ(mgd.basis_species_name[sp.second], sp.first);
585
586 ASSERT_EQ(mgd.eqm_species_index.size(), (std::size_t)9);
587 for (const auto & sp : mgd.eqm_species_index)
588 ASSERT_EQ(mgd.eqm_species_name[sp.second], sp.first);
589
590 ASSERT_EQ(mgd.kin_species_index.size(), (std::size_t)3);
591 for (const auto & sp : mgd.kin_species_index)
592 ASSERT_EQ(mgd.kin_species_name[sp.second], sp.first);
593}
594
600TEST(PertinentGeochemicalSystemTest, names2)
601{
602 GeochemicalDatabaseReader database("database/moose_testdb.json");
603
604 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--
605 PertinentGeochemicalSystem model(database,
606 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
607 {},
608 {"O2(g)"},
609 {"Calcite_asdf", "Calcite"},
610 {"CH4(aq)"},
611 {">(s)FeOCa+", ">(s)FeO-"},
612 "O2(aq)",
613 "e-");
614 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
615
616 ASSERT_EQ(mgd.basis_species_index.size(), (std::size_t)6);
617 for (const auto & sp : mgd.basis_species_index)
618 ASSERT_EQ(mgd.basis_species_name[sp.second], sp.first);
619
620 ASSERT_EQ(mgd.eqm_species_index.size(), (std::size_t)7);
621 for (const auto & sp : mgd.eqm_species_index)
622 ASSERT_EQ(mgd.eqm_species_name[sp.second], sp.first);
623
624 ASSERT_EQ(mgd.kin_species_index.size(), (std::size_t)5);
625 for (const auto & sp : mgd.kin_species_index)
626 ASSERT_EQ(mgd.kin_species_name[sp.second], sp.first);
627}
628
630TEST(PertinentGeochemicalSystemTest, charge)
631{
632 GeochemicalDatabaseReader database("database/moose_testdb.json");
633
634 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
635 // >(s)FeO-, e-
636 PertinentGeochemicalSystem model(database,
637 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
638 {"Calcite"},
639 {},
640 {"Calcite_asdf"},
641 {"CH4(aq)"},
642 {">(s)FeOCa+"},
643 "O2(aq)",
644 "e-");
645 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
646
647 std::map<std::string, Real> charge_gold;
648 charge_gold["H2O"] = 0.0;
649 charge_gold["H+"] = 1.0;
650 charge_gold["HCO3-"] = -1.0;
651 charge_gold["O2(aq)"] = 0.0;
652 charge_gold["Ca++"] = 2.0;
653 charge_gold[">(s)FeOH"] = 0.0;
654 charge_gold["CO2(aq)"] = 0.0;
655 charge_gold["CO3--"] = -2.0;
656 charge_gold["CaCO3"] = 0.0;
657 charge_gold["CaOH+"] = 1.0;
658 charge_gold["OH-"] = -1.0;
659 charge_gold["(O-phth)--"] = -2.0;
660 charge_gold[">(s)FeO-"] = -1.0;
661 charge_gold[">(s)FeOCa+"] = -1.0;
662 charge_gold["Calcite"] = 0.0;
663 charge_gold["e-"] = -1.0;
664 charge_gold["Calcite_asdf"] = 0.0;
665 charge_gold["CH4(aq)"] = 0.0;
666 for (const auto & sp : mgd.basis_species_index)
667 ASSERT_EQ(mgd.basis_species_charge[sp.second], charge_gold[sp.first]);
668 for (const auto & sp : mgd.eqm_species_index)
669 ASSERT_EQ(mgd.eqm_species_charge[sp.second], charge_gold[sp.first]);
670 for (const auto & sp : mgd.kin_species_index)
671 ASSERT_EQ(mgd.kin_species_charge[sp.second], charge_gold[sp.first]);
672}
673
675TEST(PertinentGeochemicalSystemTest, radius)
676{
677 GeochemicalDatabaseReader database("database/moose_testdb.json");
678
679 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
680 // >(s)FeO-, >(s)FeOCa+, e-
681 PertinentGeochemicalSystem model(database,
682 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
683 {"Calcite"},
684 {},
685 {},
686 {"CH4(aq)"},
687 {},
688 "O2(aq)",
689 "e-");
690 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
691
692 std::map<std::string, Real> radius_gold;
693 radius_gold["H2O"] = 0.0;
694 radius_gold["H+"] = 9.0;
695 radius_gold["HCO3-"] = 4.5;
696 radius_gold["O2(aq)"] = -0.5;
697 radius_gold["Ca++"] = 6.0;
698 radius_gold[">(s)FeOH"] = 0.0;
699 radius_gold["CO2(aq)"] = 4.0;
700 radius_gold["CO3--"] = 4.5;
701 radius_gold["CaCO3"] = 4.0;
702 radius_gold["CaOH+"] = 4.0;
703 radius_gold["OH-"] = 3.5;
704 radius_gold["(O-phth)--"] = 4.0;
705 radius_gold[">(s)FeO-"] = -1.5;
706 radius_gold[">(s)FeOCa+"] = -1.5;
707 radius_gold["Calcite"] = 0.0;
708 radius_gold["e-"] = 0.0;
709 for (const auto & sp : mgd.basis_species_index)
710 ASSERT_EQ(mgd.basis_species_radius[sp.second], radius_gold[sp.first]);
711 for (const auto & sp : mgd.eqm_species_index)
712 ASSERT_EQ(mgd.eqm_species_radius[sp.second], radius_gold[sp.first]);
713}
714
716TEST(PertinentGeochemicalSystemTest, molecular_weight)
717{
718 GeochemicalDatabaseReader database("database/moose_testdb.json");
719
720 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
721 // >(s)FeO-, >(s)FeOCa+, e-
722 PertinentGeochemicalSystem model(database,
723 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
724 {"Calcite"},
725 {},
726 {"Calcite_asdf"},
727 {"CH4(aq)"},
728 {">(s)FeOCa+"},
729 "O2(aq)",
730 "e-");
731 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
732
733 std::map<std::string, Real> molecular_weight_gold;
734 molecular_weight_gold["H2O"] = 18.0152;
735 molecular_weight_gold["H+"] = 1.0079;
736 molecular_weight_gold["HCO3-"] = 61.0171;
737 molecular_weight_gold["O2(aq)"] = 31.9988;
738 molecular_weight_gold["Ca++"] = 40.0800;
739 molecular_weight_gold[">(s)FeOH"] = 72.8543;
740 molecular_weight_gold["CO2(aq)"] = 44.0098;
741 molecular_weight_gold["CO3--"] = 60.0092;
742 molecular_weight_gold["CaCO3"] = 100.0892;
743 molecular_weight_gold["CaOH+"] = 57.0873;
744 molecular_weight_gold["OH-"] = 17.0073;
745 molecular_weight_gold["(O-phth)--"] = 164.1172;
746 molecular_weight_gold[">(s)FeO-"] = 71.8464;
747 molecular_weight_gold[">(s)FeOCa+"] = 279.7144;
748 molecular_weight_gold["Calcite"] = 100.0892;
749 molecular_weight_gold["e-"] = 0.0;
750 molecular_weight_gold["Calcite_asdf"] = 111.0892;
751 molecular_weight_gold["CH4(aq)"] = 16.0426;
752 molecular_weight_gold[">(s)FeOCa+"] = 279.7144;
753 for (const auto & sp : mgd.basis_species_index)
754 ASSERT_EQ(mgd.basis_species_molecular_weight[sp.second], molecular_weight_gold[sp.first]);
755 for (const auto & sp : mgd.eqm_species_index)
756 ASSERT_EQ(mgd.eqm_species_molecular_weight[sp.second], molecular_weight_gold[sp.first]);
757 for (const auto & sp : mgd.kin_species_index)
758 ASSERT_EQ(mgd.kin_species_molecular_weight[sp.second], molecular_weight_gold[sp.first]);
759}
760
762TEST(PertinentGeochemicalSystemTest, molecular_volume)
763{
764 GeochemicalDatabaseReader database("database/moose_testdb.json");
765
766 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
767 // >(s)FeO-, >(s)FeOCa+, e-
768 PertinentGeochemicalSystem model(database,
769 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
770 {"Calcite"},
771 {},
772 {"Calcite_asdf"},
773 {"CH4(aq)"},
774 {">(s)FeOCa+"},
775 "O2(aq)",
776 "e-");
777 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
778
779 std::map<std::string, Real> molecular_volume_gold;
780 molecular_volume_gold["H2O"] = 0.0;
781 molecular_volume_gold["H+"] = 0.0;
782 molecular_volume_gold["HCO3-"] = 0.0;
783 molecular_volume_gold["O2(aq)"] = 0.0;
784 molecular_volume_gold["Ca++"] = 0.0;
785 molecular_volume_gold[">(s)FeOH"] = 0.0;
786 molecular_volume_gold["CO2(aq)"] = 0.0;
787 molecular_volume_gold["CO3--"] = 0.0;
788 molecular_volume_gold["CaCO3"] = 0.0;
789 molecular_volume_gold["CaOH+"] = 0.0;
790 molecular_volume_gold["OH-"] = 0.0;
791 molecular_volume_gold["(O-phth)--"] = 0.0;
792 molecular_volume_gold[">(s)FeO-"] = 0.0;
793 molecular_volume_gold[">(s)FeOCa+"] = 0.0;
794 molecular_volume_gold["Calcite"] = 36.9340;
795 molecular_volume_gold["e-"] = 0.0;
796 molecular_volume_gold["Calcite_asdf"] = 136.9340;
797 molecular_volume_gold["CH4(aq)"] = 0.0;
798 molecular_volume_gold[">(s)FeOCa+"] = 0.0;
799 for (const auto & sp : mgd.basis_species_index)
800 ASSERT_EQ(mgd.basis_species_molecular_volume[sp.second], molecular_volume_gold[sp.first]);
801 for (const auto & sp : mgd.eqm_species_index)
802 ASSERT_EQ(mgd.eqm_species_molecular_volume[sp.second], molecular_volume_gold[sp.first]);
803 for (const auto & sp : mgd.kin_species_index)
804 ASSERT_EQ(mgd.kin_species_molecular_volume[sp.second], molecular_volume_gold[sp.first]);
805}
806
808TEST(PertinentGeochemicalSystemTest, surfaceComplexationInfo)
809{
810 GeochemicalDatabaseReader database("database/moose_testdb.json");
811
812 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
813 // >(s)FeO-, >(s)FeOCa+, e-
814 PertinentGeochemicalSystem model1(database,
815 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
816 {"Calcite"},
817 {},
818 {},
819 {"CH4(aq)"},
820 {},
821 "O2(aq)",
822 "e-");
823 ModelGeochemicalDatabase mgd1 = model1.modelGeochemicalDatabase();
824
825 ASSERT_EQ(mgd1.surface_complexation_info.size(), (std::size_t)0);
826
827 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
828 // >(s)FeO-, >(s)FeOCa+, e-
829 PertinentGeochemicalSystem model2(database,
830 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH", ">(w)FeOH"},
831 {"Fe(OH)3(ppd)"},
832 {},
833 {},
834 {},
835 {},
836 "O2(aq)",
837 "e-");
838 ModelGeochemicalDatabase mgd2 = model2.modelGeochemicalDatabase();
839
840 ASSERT_EQ(mgd2.surface_complexation_info.count("Fe(OH)3(ppd)"), (std::size_t)1);
841 ASSERT_EQ(mgd2.surface_complexation_info["Fe(OH)3(ppd)"].surface_area, 600.0);
842 ASSERT_EQ(mgd2.surface_complexation_info["Fe(OH)3(ppd)"].sorption_sites[">(s)FeOH"], 0.005);
843 ASSERT_EQ(mgd2.surface_complexation_info["Fe(OH)3(ppd)"].sorption_sites[">(w)FeOH"], 0.2);
844
845 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
846 // >(s)FeO-, >(s)FeOCa+, e-
847 PertinentGeochemicalSystem model3(database,
848 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH", ">(w)FeOH"},
849 {},
850 {},
851 {"Goethite"},
852 {},
853 {},
854 "O2(aq)",
855 "e-");
856 ModelGeochemicalDatabase mgd3 = model3.modelGeochemicalDatabase();
857
858 ASSERT_EQ(mgd3.surface_complexation_info.count("Goethite"), (std::size_t)1);
859 ASSERT_EQ(mgd3.surface_complexation_info["Goethite"].surface_area, 60.0);
860 ASSERT_EQ(mgd3.surface_complexation_info["Goethite"].sorption_sites[">(s)FeOH"], 0.05);
861 ASSERT_EQ(mgd3.surface_complexation_info["Goethite"].sorption_sites[">(w)FeOH"], 0.222);
862}
863
865TEST(PertinentGeochemicalSystemTest, surfaceComplexationRepeatedException)
866{
867 GeochemicalDatabaseReader database("database/moose_testdb.json");
868
869 try
870 {
871 PertinentGeochemicalSystem model3(database,
872 {"H2O", "H+", "O2(aq)", "Fe++", ">(s)FeOH", ">(w)FeOH"},
873 {"Goethite", "Fe(OH)3(ppd)"},
874 {},
875 {},
876 {},
877 {},
878 "O2(aq)",
879 "e-");
880 FAIL() << "Missing expected exception.";
881 }
882 catch (const std::exception & e)
883 {
884 std::string msg(e.what());
885 ASSERT_TRUE(msg.find("The sorbing site >(s)FeOH appears in more than one sorbing mineral") !=
886 std::string::npos)
887 << "Failed with unexpected error message: " << msg;
888 }
889}
890
892TEST(PertinentGeochemicalSystemTest, excessSorbingSitesException)
893{
894 GeochemicalDatabaseReader database("database/moose_testdb.json");
895
896 try
897 {
898 PertinentGeochemicalSystem model2(database,
899 {"H2O", "H+", "Fe+++", "sorbsite1", "sorbsite2"},
900 {"problematic_sorber"},
901 {},
902 {},
903 {},
904 {},
905 "O2(aq)",
906 "e-");
907 FAIL() << "Missing expected exception.";
908 }
909 catch (const std::exception & e)
910 {
911 std::string msg(e.what());
912 ASSERT_TRUE(msg.find("It is an error for any equilibrium species (such as problem_eqm) to have "
913 "a reaction involving more than one sorbing site") != std::string::npos)
914 << "Failed with unexpected error message: " << msg;
915 }
916}
917
919TEST(PertinentGeochemicalSystemTest, surfaceSorptionBuilding)
920{
921 GeochemicalDatabaseReader database("database/moose_testdb.json");
922
923 PertinentGeochemicalSystem modelC(
924 database, {"H2O", "H+", "Ca++", "HCO3-"}, {"Calcite"}, {}, {}, {}, {}, "O2(aq)", "e-");
925 ModelGeochemicalDatabase mgdC = modelC.modelGeochemicalDatabase();
926
927 EXPECT_EQ(mgdC.surface_sorption_name.size(), (std::size_t)0);
928 EXPECT_EQ(mgdC.surface_sorption_area.size(), (std::size_t)0);
929 for (unsigned j = 0; j < mgdC.eqm_species_name.size(); ++j)
930 EXPECT_EQ(mgdC.surface_sorption_related[j], false);
931
932 PertinentGeochemicalSystem model2(database,
933 {"H2O", "H+", "Fe+++", ">(s)FeOH", ">(w)FeOH"},
934 {"Fe(OH)3(ppd)fake", "Goethite"},
935 {},
936 {},
937 {},
938 {},
939 "O2(aq)",
940 "e-");
941 ModelGeochemicalDatabase mgd2 = model2.modelGeochemicalDatabase();
942 EXPECT_EQ(mgd2.surface_complexation_info.count("Goethite"), (std::size_t)1);
943 EXPECT_EQ(mgd2.surface_sorption_name.size(), (std::size_t)1);
944 EXPECT_EQ(mgd2.surface_sorption_name[0], "Goethite");
945 EXPECT_EQ(mgd2.surface_sorption_area.size(), (std::size_t)1);
946 EXPECT_EQ(mgd2.surface_sorption_area[0], 60.0);
947 EXPECT_EQ(mgd2.surface_sorption_related.size(), mgd2.eqm_species_name.size());
948 EXPECT_EQ(mgd2.surface_sorption_number.size(), mgd2.eqm_species_name.size());
949 // Eqm species are: OH- >(s)FeO- Fe(OH)3(ppd)fake Goethite
950 EXPECT_EQ(mgd2.eqm_species_index.count(">(s)FeO-"), (std::size_t)1);
951 const unsigned posn = mgd2.eqm_species_index.at(">(s)FeO-");
952 for (unsigned j = 0; j < mgd2.eqm_species_name.size(); ++j)
953 if (j == posn)
954 EXPECT_TRUE(mgd2.surface_sorption_related[j]);
955 else
956 EXPECT_FALSE(mgd2.surface_sorption_related[j]);
957 EXPECT_EQ(mgd2.surface_sorption_number[posn], (unsigned int)0);
958}
959
961TEST(PertinentGeochemicalSystemTest, GasChi)
962{
963 GeochemicalDatabaseReader database("database/moose_testdb.json");
964
965 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
966 // >(s)FeO-, >(s)FeOCa+, e-
967 PertinentGeochemicalSystem model1(database,
968 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
969 {"Calcite"},
970 {},
971 {},
972 {"CH4(aq)"},
973 {},
974 "O2(aq)",
975 "e-");
976 ModelGeochemicalDatabase mgd1 = model1.modelGeochemicalDatabase();
977
978 ASSERT_EQ(mgd1.gas_chi.size(), (std::size_t)0);
979
980 PertinentGeochemicalSystem model2(database,
981 {"H2O", "Ca++", "H+", "HCO3-", "O2(aq)"},
982 {"Calcite"},
983 {"CH4(g)"},
984 {},
985 {},
986 {},
987 "O2(aq)",
988 "e-");
989 ModelGeochemicalDatabase mgd2 = model2.modelGeochemicalDatabase();
990
991 ASSERT_EQ(mgd2.gas_chi.count("CH4(g)"), (std::size_t)1);
992 ASSERT_EQ(mgd2.gas_chi["CH4(g)"][0], -537.779);
993 ASSERT_EQ(mgd2.gas_chi["CH4(g)"][1], 1.54946);
994 ASSERT_EQ(mgd2.gas_chi["CH4(g)"][2], -.000927827);
995 ASSERT_EQ(mgd2.gas_chi["CH4(g)"][3], 1.20861);
996 ASSERT_EQ(mgd2.gas_chi["CH4(g)"][4], -.00370814);
997 ASSERT_EQ(mgd2.gas_chi["CH4(g)"][5], 3.33804e-6);
998}
999
1003TEST(PertinentGeochemicalSystemTest, stoichiometry1)
1004{
1005 GeochemicalDatabaseReader database("database/moose_testdb.json");
1006
1007 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--
1008 PertinentGeochemicalSystem model(database,
1009 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
1010 {"Calcite"},
1011 {},
1012 {"Calcite_asdf"},
1013 {"CH4(aq)"},
1014 {">(s)FeO-", ">(s)FeOCa+"},
1015 "O2(aq)",
1016 "e-");
1017 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1018
1019 ASSERT_EQ(mgd.eqm_species_index.size(), (std::size_t)7);
1020 for (const auto & sp : {"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-", "(O-phth)--", "Calcite"})
1021 ASSERT_EQ(mgd.eqm_species_index.count(sp), (std::size_t)1);
1022
1023 std::map<std::string, DenseMatrix<Real>> stoi_gold;
1024 for (const auto & sp : {"CO2(aq)",
1025 "CO3--",
1026 "CaCO3",
1027 "CaOH+",
1028 "OH-",
1029 "(O-phth)--",
1030 ">(s)FeO-",
1031 ">(s)FeOCa+",
1032 "Calcite",
1033 "Calcite_asdf",
1034 "CH4(aq)"})
1035 stoi_gold[sp] = DenseMatrix<Real>(1, 6);
1036 // remember the order of primaries: {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
1037 stoi_gold["CO2(aq)"](0, 0) = -1;
1038 stoi_gold["CO2(aq)"](0, 1) = 1;
1039 stoi_gold["CO2(aq)"](0, 2) = 1;
1040 stoi_gold["CO3--"](0, 1) = -1;
1041 stoi_gold["CO3--"](0, 2) = 1;
1042 stoi_gold["CaCO3"](0, 4) = 1;
1043 stoi_gold["CaCO3"](0, 2) = 1;
1044 stoi_gold["CaCO3"](0, 1) = -1;
1045 stoi_gold["CaOH+"](0, 4) = 1;
1046 stoi_gold["CaOH+"](0, 0) = 1;
1047 stoi_gold["CaOH+"](0, 1) = -1;
1048 stoi_gold["OH-"](0, 0) = 1;
1049 stoi_gold["OH-"](0, 1) = -1;
1050 stoi_gold["(O-phth)--"](0, 0) = -5;
1051 stoi_gold["(O-phth)--"](0, 2) = 8;
1052 stoi_gold["(O-phth)--"](0, 1) = 6;
1053 stoi_gold["(O-phth)--"](0, 3) = -7.5;
1054 stoi_gold[">(s)FeO-"](0, 5) = 1;
1055 stoi_gold[">(s)FeO-"](0, 1) = -1;
1056 stoi_gold[">(s)FeOCa+"](0, 5) = 1;
1057 stoi_gold[">(s)FeOCa+"](0, 4) = 1;
1058 stoi_gold[">(s)FeOCa+"](0, 1) = -1;
1059 stoi_gold["Calcite"](0, 4) = 1;
1060 stoi_gold["Calcite"](0, 2) = 1;
1061 stoi_gold["Calcite"](0, 1) = -1;
1062 stoi_gold["Calcite_asdf"](0, 4) = 2;
1063 stoi_gold["Calcite_asdf"](0, 2) = 1;
1064 stoi_gold["Calcite_asdf"](0, 1) = -1;
1065 // remember the order of primaries: {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
1066 stoi_gold["CH4(aq)"](0, 0) = 1;
1067 stoi_gold["CH4(aq)"](0, 1) = 1;
1068 stoi_gold["CH4(aq)"](0, 2) = 1;
1069 stoi_gold["CH4(aq)"](0, 3) = -2;
1070
1071 for (const auto & sp : {"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-", "(O-phth)--", "Calcite"})
1072 {
1073 const unsigned row = mgd.eqm_species_index[sp];
1074 ASSERT_EQ(mgd.eqm_stoichiometry.sub_matrix(row, 1, 0, 6), stoi_gold[sp]);
1075 }
1076 for (const auto & sp : {"Calcite_asdf", "CH4(aq)", ">(s)FeO-", ">(s)FeOCa+"})
1077 {
1078 const unsigned row = mgd.kin_species_index[sp];
1079 ASSERT_EQ(mgd.kin_stoichiometry.sub_matrix(row, 1, 0, 6), stoi_gold[sp]);
1080 }
1081}
1082
1084TEST(PertinentGeochemicalSystemTest, log10K1)
1085{
1086 GeochemicalDatabaseReader database("database/moose_testdb.json");
1087
1088 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, (O-phth)--,
1089 // >(s)FeO-, >(s)FeOCa+
1090 PertinentGeochemicalSystem model(database,
1091 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH"},
1092 {"Calcite"},
1093 {},
1094 {},
1095 {"CH4(aq)"},
1096 {},
1097 "O2(aq)",
1098 "e-");
1099 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1100
1101 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 0), -6.5570);
1102 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 1), -6.3660);
1103 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 2), -6.3325);
1104 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 3), -6.4330);
1105 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 4), -6.7420);
1106 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 5), -7.1880);
1107 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 6), -7.7630);
1108 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 7), -8.4650);
1109 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CO3--"], 0), 10.6169);
1110 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CaCO3"], 0), 7.5520);
1111 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["CaOH+"], 0), 13.7095);
1112 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["OH-"], 0), 14.9325);
1113 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["(O-phth)--"], 0), 594.3211);
1114 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 0), 8.9300);
1115 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeOCa+"], 0), 1.7200);
1116 ASSERT_EQ(mgd.eqm_log10K(mgd.eqm_species_index["Calcite"], 0), 2.0683);
1117}
1118
1124TEST(PertinentGeochemicalSystemTest, stoichiometry2)
1125{
1126 GeochemicalDatabaseReader database("database/moose_testdb.json");
1127
1128 // The following system has secondary species: CO2(aq), CO3--, OH-, (O-phth)--, CH4(aq), Fe+++,
1129 // >(s)FeO-
1130 PertinentGeochemicalSystem model(database,
1131 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1132 {"Fe(OH)3(ppd)fake"},
1133 {"CH4(g)fake"},
1134 {"Fe(OH)3(ppd)"},
1135 {},
1136 {},
1137 "O2(aq)",
1138 "e-");
1139 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1140
1141 ASSERT_EQ(mgd.eqm_species_index.size(), (std::size_t)9);
1142 for (const auto & sp : {"CO2(aq)",
1143 "CO3--",
1144 "OH-",
1145 "(O-phth)--",
1146 "CH4(aq)",
1147 "Fe+++",
1148 ">(s)FeO-",
1149 "Fe(OH)3(ppd)fake",
1150 "CH4(g)fake"})
1151 ASSERT_EQ(mgd.eqm_species_index.count(sp), (std::size_t)1);
1152
1153 std::map<std::string, DenseMatrix<Real>> stoi_gold;
1154 for (const auto & sp : {"CO2(aq)",
1155 "CO3--",
1156 "OH-",
1157 "(O-phth)--",
1158 "CH4(aq)",
1159 "Fe+++",
1160 ">(s)FeO-",
1161 "Fe(OH)3(ppd)fake",
1162 "Fe(OH)3(ppd)",
1163 "CH4(g)fake"})
1164 stoi_gold[sp] = DenseMatrix<Real>(1, 7);
1165 // remember the order of primaries:
1166 // {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"}
1167 stoi_gold["CO2(aq)"](0, 0) = -1;
1168 stoi_gold["CO2(aq)"](0, 1) = 1;
1169 stoi_gold["CO2(aq)"](0, 5) = 1;
1170 stoi_gold["CO3--"](0, 5) = 1;
1171 stoi_gold["CO3--"](0, 1) = -1;
1172 stoi_gold["OH-"](0, 0) = 1;
1173 stoi_gold["OH-"](0, 1) = -1;
1174 stoi_gold["(O-phth)--"](0, 0) = -5;
1175 stoi_gold["(O-phth)--"](0, 5) = 8;
1176 stoi_gold["(O-phth)--"](0, 1) = 6;
1177 stoi_gold["(O-phth)--"](0, 6) = -7.5;
1178 stoi_gold["CH4(aq)"](0, 0) = 1;
1179 stoi_gold["CH4(aq)"](0, 1) = 1;
1180 stoi_gold["CH4(aq)"](0, 5) = 1;
1181 stoi_gold["CH4(aq)"](0, 6) = -2;
1182 stoi_gold["Fe+++"](0, 0) = -0.5;
1183 stoi_gold["Fe+++"](0, 4) = 1;
1184 stoi_gold["Fe+++"](0, 1) = 1;
1185 stoi_gold["Fe+++"](0, 6) = 0.25;
1186 stoi_gold[">(s)FeO-"](0, 2) = 1;
1187 stoi_gold[">(s)FeO-"](0, 1) = -1;
1188 stoi_gold["Fe(OH)3(ppd)fake"](0, 1) = -1;
1189 stoi_gold["Fe(OH)3(ppd)fake"](0, 0) = 2;
1190 stoi_gold["Fe(OH)3(ppd)fake"](0, 4) = 2;
1191 stoi_gold["Fe(OH)3(ppd)fake"](0, 6) = 0.5;
1192 stoi_gold["CH4(g)fake"](0, 0) = 3;
1193 stoi_gold["CH4(g)fake"](0, 4) = -2;
1194 stoi_gold["CH4(g)fake"](0, 5) = 3.5;
1195 stoi_gold["CH4(g)fake"](0, 6) = -4.5;
1196 stoi_gold["Fe(OH)3(ppd)"](0, 1) = -2;
1197 stoi_gold["Fe(OH)3(ppd)"](0, 4) = 1;
1198 stoi_gold["Fe(OH)3(ppd)"](0, 0) = 2.5;
1199 stoi_gold["Fe(OH)3(ppd)"](0, 6) = 0.25;
1200
1201 for (const auto & sp : {"CO2(aq)",
1202 "CO3--",
1203 "OH-",
1204 "(O-phth)--",
1205 "CH4(aq)",
1206 "Fe+++",
1207 ">(s)FeO-",
1208 "Fe(OH)3(ppd)fake",
1209 "CH4(g)fake"})
1210 {
1211 const unsigned row = mgd.eqm_species_index[sp];
1212 ASSERT_EQ(mgd.eqm_stoichiometry.sub_matrix(row, 1, 0, 7), stoi_gold[sp]);
1213 }
1214 ASSERT_EQ(mgd.kin_stoichiometry.sub_matrix(0, 1, 0, 7), stoi_gold["Fe(OH)3(ppd)"]);
1215}
1216
1222TEST(PertinentGeochemicalSystemTest, stoichiometry3)
1223{
1224 GeochemicalDatabaseReader database("database/moose_testdb.json");
1225
1226 // The following system has secondary species: CO2(aq), CO3--, OH-, CH4(aq), Fe+++
1227 PertinentGeochemicalSystem model(database,
1228 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1229 {},
1230 {"CH4(g)fake"},
1231 {"Fe(OH)3(ppd)", "Fe(OH)3(ppd)fake"},
1232 {"(O-phth)--"},
1233 {">(s)FeO-"},
1234 "O2(aq)",
1235 "e-");
1236 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1237
1238 ASSERT_EQ(mgd.eqm_species_index.size(), (std::size_t)6);
1239 for (const auto & sp : {"CO2(aq)", "CO3--", "OH-", "CH4(aq)", "Fe+++", "CH4(g)fake"})
1240 ASSERT_EQ(mgd.eqm_species_index.count(sp), (std::size_t)1);
1241
1242 std::map<std::string, DenseMatrix<Real>> stoi_gold;
1243 for (const auto & sp : {"CO2(aq)",
1244 "CO3--",
1245 "OH-",
1246 "(O-phth)--",
1247 "CH4(aq)",
1248 "Fe+++",
1249 ">(s)FeO-",
1250 "Fe(OH)3(ppd)fake",
1251 "Fe(OH)3(ppd)",
1252 "CH4(g)fake"})
1253 stoi_gold[sp] = DenseMatrix<Real>(1, 7);
1254 // remember the order of primaries:
1255 // {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"}
1256 stoi_gold["CO2(aq)"](0, 0) = -1;
1257 stoi_gold["CO2(aq)"](0, 1) = 1;
1258 stoi_gold["CO2(aq)"](0, 5) = 1;
1259 stoi_gold["CO3--"](0, 5) = 1;
1260 stoi_gold["CO3--"](0, 1) = -1;
1261 stoi_gold["OH-"](0, 0) = 1;
1262 stoi_gold["OH-"](0, 1) = -1;
1263 stoi_gold["(O-phth)--"](0, 0) = -5;
1264 stoi_gold["(O-phth)--"](0, 5) = 8;
1265 stoi_gold["(O-phth)--"](0, 1) = 6;
1266 stoi_gold["(O-phth)--"](0, 6) = -7.5;
1267 stoi_gold["CH4(aq)"](0, 0) = 1;
1268 stoi_gold["CH4(aq)"](0, 1) = 1;
1269 stoi_gold["CH4(aq)"](0, 5) = 1;
1270 stoi_gold["CH4(aq)"](0, 6) = -2;
1271 stoi_gold["Fe+++"](0, 0) = -0.5;
1272 stoi_gold["Fe+++"](0, 4) = 1;
1273 stoi_gold["Fe+++"](0, 1) = 1;
1274 stoi_gold["Fe+++"](0, 6) = 0.25;
1275 stoi_gold[">(s)FeO-"](0, 2) = 1;
1276 stoi_gold[">(s)FeO-"](0, 1) = -1;
1277 stoi_gold["Fe(OH)3(ppd)fake"](0, 1) = -1;
1278 stoi_gold["Fe(OH)3(ppd)fake"](0, 0) = 2;
1279 stoi_gold["Fe(OH)3(ppd)fake"](0, 4) = 2;
1280 stoi_gold["Fe(OH)3(ppd)fake"](0, 6) = 0.5;
1281 stoi_gold["CH4(g)fake"](0, 0) = 3;
1282 stoi_gold["CH4(g)fake"](0, 4) = -2;
1283 stoi_gold["CH4(g)fake"](0, 5) = 3.5;
1284 stoi_gold["CH4(g)fake"](0, 6) = -4.5;
1285 stoi_gold["Fe(OH)3(ppd)"](0, 1) = -2;
1286 stoi_gold["Fe(OH)3(ppd)"](0, 4) = 1;
1287 stoi_gold["Fe(OH)3(ppd)"](0, 0) = 2.5;
1288 stoi_gold["Fe(OH)3(ppd)"](0, 6) = 0.25;
1289
1290 for (const auto & sp : {"CO2(aq)", "CO3--", "OH-", "CH4(aq)", "Fe+++", "CH4(g)fake"})
1291 {
1292 const unsigned row = mgd.eqm_species_index[sp];
1293 ASSERT_EQ(mgd.eqm_stoichiometry.sub_matrix(row, 1, 0, 7), stoi_gold[sp]);
1294 }
1295
1296 for (const auto & sp : {"Fe(OH)3(ppd)", "Fe(OH)3(ppd)fake", "(O-phth)--", ">(s)FeO-"})
1297 {
1298 const unsigned row = mgd.kin_species_index[sp];
1299 ASSERT_EQ(mgd.kin_stoichiometry.sub_matrix(row, 1, 0, 7), stoi_gold[sp]);
1300 }
1301}
1302
1308TEST(PertinentGeochemicalSystemTest, log10K2)
1309{
1310 GeochemicalDatabaseReader database("database/moose_testdb.json");
1311
1312 // The following system has secondary species: CO2(aq), CO3--, OH-, (O-phth)--, CH4(aq), Fe+++,
1313 // >(s)FeO-
1314 PertinentGeochemicalSystem model(database,
1315 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1316 {"Fe(OH)3(ppd)fake"},
1317 {"CH4(g)fake"},
1318 {},
1319 {},
1320 {},
1321 "O2(aq)",
1322 "e-");
1323 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1324
1325 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CO2(aq)"], 0), -6.5570, eps);
1326 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CO3--"], 0), 10.6169, eps);
1327 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["OH-"], 0), 14.9325, eps);
1328 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["(O-phth)--"], 0), 594.3211, eps);
1329 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(aq)"], 0), 157.8920, eps);
1330 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["Fe+++"], 0), -10.0553, eps);
1331 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 0), 8.93, eps);
1332 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 1), 8.93 - 0.3 * (25 - 0), eps);
1333 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 2), 8.93 - 0.3 * (60 - 0), eps);
1334 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 3), 8.93 - 0.3 * (100 - 0), eps);
1335 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 4), 8.93 - 0.3 * (150 - 0), eps);
1336 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 5), 8.93 - 0.3 * (200 - 0), eps);
1337 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 6), 8.93 - 0.3 * (250 - 0), eps);
1338 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index[">(s)FeO-"], 7), 8.93 - 0.3 * (300 - 0), eps);
1339 ASSERT_NEAR(
1340 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 0), 6.1946 + 2 * (-10.0553), eps);
1341 ASSERT_NEAR(
1342 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 1), 4.8890 + 2 * (-8.4878), eps);
1343 ASSERT_NEAR(
1344 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 2), 3.4608 + 2 * (-6.6954), eps);
1345 ASSERT_NEAR(
1346 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 3), 2.2392 + 2 * (-5.0568), eps);
1347 ASSERT_NEAR(
1348 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 4), 1.1150 + 2 * (-3.4154), eps);
1349 ASSERT_NEAR(
1350 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 5), 0.2446 + 2 * (-2.0747), eps);
1351 ASSERT_NEAR(
1352 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 6), -0.5504 + 2 * (-0.8908), eps);
1353 ASSERT_NEAR(
1354 mgd.eqm_log10K(mgd.eqm_species_index["Fe(OH)3(ppd)fake"], 7), -1.5398 + 2 * (0.2679), eps);
1355 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 0),
1356 -2.6487 + 2 * 157.8920 - 2 * (-10.0553),
1357 eps);
1358 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 1),
1359 -2.8202 + 2 * 144.1080 - 2 * (-8.4878),
1360 eps);
1361 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 2),
1362 -2.9329 + 2 * 127.9360 - 2 * (-6.6954),
1363 eps);
1364 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 3),
1365 -2.9446 + 2 * 112.8800 - 2 * (-5.0568),
1366 eps);
1367 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 4),
1368 -2.9163 + 2 * 97.7060 - 2 * (-3.4154),
1369 eps);
1370 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 5),
1371 -2.7253 + 2 * 85.2880 - 2 * (-2.0747),
1372 eps);
1373 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 6),
1374 -2.4643 + 2 * 74.7500 - 2 * (-0.8908),
1375 eps);
1376 ASSERT_NEAR(mgd.eqm_log10K(mgd.eqm_species_index["CH4(g)fake"], 7),
1377 -2.1569 + 2 * 65.6500 - 2 * (0.2679),
1378 eps);
1379}
1380
1385TEST(PertinentGeochemicalSystemTest, secondarySpecies2)
1386{
1387 GeochemicalDatabaseReader database("database/moose_testdb.json");
1388
1389 // The following system has secondary species: CO2(aq), CO3--, CaCO3, CaOH+, OH-, >(s)FeO-,
1390 // >(s)FeOCa+
1391 PertinentGeochemicalSystem model(
1392 database,
1393 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH", "(O-phth)--"},
1394 {"Calcite"},
1395 {},
1396 {},
1397 {"CH4(aq)"},
1398 {},
1399 "O2(aq)",
1400 "e-");
1401 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1402
1403 ASSERT_EQ(mgd.eqm_species_index.size(), (std::size_t)8);
1404 for (const auto & sp :
1405 {"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-", ">(s)FeO-", ">(s)FeOCa+", "Calcite"})
1406 ASSERT_EQ(mgd.eqm_species_index.count(sp), (std::size_t)1);
1407}
1408
1410TEST(PertinentGeochemicalSystemTest, isMineral)
1411{
1412 GeochemicalDatabaseReader database("database/moose_testdb.json");
1413
1414 // The following system has secondary species: CO2(aq), CO3--, OH-, (O-phth)--, CH4(aq), Fe+++,
1415 // >(s)FeO-, e-
1416 PertinentGeochemicalSystem model(database,
1417 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1418 {"Fe(OH)3(ppd)fake"},
1419 {"CH4(g)fake"},
1420 {},
1421 {},
1422 {},
1423 "O2(aq)",
1424 "e-");
1425 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1426
1427 for (const auto & species : mgd.basis_species_index)
1428 ASSERT_EQ(mgd.basis_species_mineral[species.second], false);
1429 for (const auto & species : mgd.eqm_species_index)
1430 if (species.first == "Fe(OH)3(ppd)fake")
1431 ASSERT_EQ(mgd.eqm_species_mineral[species.second], true);
1432 else
1433 ASSERT_EQ(mgd.eqm_species_mineral[species.second], false);
1434
1435 PertinentGeochemicalSystem model2(
1436 database,
1437 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1438 {},
1439 {"CH4(g)fake"},
1440 {"Fe(OH)3(ppd)fake"},
1441 {"(O-phth)--"},
1442 {">(s)FeO-"},
1443 "O2(aq)",
1444 "e-");
1445 ModelGeochemicalDatabase mgd2 = model2.modelGeochemicalDatabase();
1446
1447 for (const auto & species : mgd2.basis_species_index)
1448 ASSERT_EQ(mgd2.basis_species_mineral[species.second], false);
1449 for (const auto & species : mgd2.eqm_species_index)
1450 ASSERT_EQ(mgd2.eqm_species_mineral[species.second], false);
1451 for (const auto & species : mgd2.kin_species_index)
1452 if (species.first == "Fe(OH)3(ppd)fake")
1453 ASSERT_EQ(mgd2.kin_species_mineral[species.second], true);
1454 else
1455 ASSERT_EQ(mgd2.kin_species_mineral[species.second], false);
1456}
1457
1459TEST(PertinentGeochemicalSystemTest, isGas)
1460{
1461 GeochemicalDatabaseReader database("database/moose_testdb.json");
1462
1463 // The following system has secondary species: CO2(aq), CO3--, OH-, (O-phth)--, CH4(aq), Fe+++,
1464 // >(s)FeO-, e-
1465 PertinentGeochemicalSystem model(database,
1466 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1467 {"Fe(OH)3(ppd)fake"},
1468 {"CH4(g)fake", "O2(g)"},
1469 {},
1470 {},
1471 {},
1472 "O2(aq)",
1473 "e-");
1474 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1475
1476 for (const auto & species : mgd.basis_species_index)
1477 ASSERT_EQ(mgd.basis_species_gas[species.second], false);
1478 for (const auto & species : mgd.eqm_species_index)
1479 if (species.first == "CH4(g)fake" || species.first == "O2(g)")
1480 ASSERT_EQ(mgd.eqm_species_gas[species.second], true);
1481 else
1482 ASSERT_EQ(mgd.eqm_species_gas[species.second], false);
1483}
1484
1486TEST(PertinentGeochemicalSystemTest, isTransported)
1487{
1488 GeochemicalDatabaseReader database("database/moose_testdb.json");
1489
1490 // The following system has secondary species: CO2(aq), CO3--, OH-, (O-phth)--, CH4(aq), Fe+++,
1491 // >(s)FeO-, e-
1492 PertinentGeochemicalSystem model(database,
1493 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1494 {"Fe(OH)3(ppd)"},
1495 {"CH4(g)fake"},
1496 {},
1497 {},
1498 {},
1499 "O2(aq)",
1500 "e-");
1501 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
1502
1503 for (const auto & species : mgd.basis_species_index)
1504 if (species.first == ">(s)FeOH" || species.first == ">(w)FeOH")
1505 EXPECT_EQ(mgd.basis_species_transported[species.second], false);
1506 else
1507 EXPECT_EQ(mgd.basis_species_transported[species.second], true);
1508 for (const auto & species : mgd.eqm_species_index)
1509 if (species.first == "Fe(OH)3(ppd)" || species.first == ">(s)FeO-")
1510 EXPECT_EQ(mgd.eqm_species_transported[species.second], false);
1511 else
1512 EXPECT_EQ(mgd.eqm_species_transported[species.second], true);
1513
1514 PertinentGeochemicalSystem model2(
1515 database,
1516 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1517 {},
1518 {"CH4(g)fake"},
1519 {"Fe(OH)3(ppd)"},
1520 {"(O-phth)--"},
1521 {">(s)FeO-"},
1522 "O2(aq)",
1523 "e-");
1524 ModelGeochemicalDatabase mgd2 = model2.modelGeochemicalDatabase();
1525
1526 for (const auto & species : mgd2.basis_species_index)
1527 if (species.first == ">(s)FeOH" || species.first == ">(w)FeOH")
1528 ASSERT_EQ(mgd2.basis_species_transported[species.second], false);
1529 else
1530 ASSERT_EQ(mgd2.basis_species_transported[species.second], true);
1531 for (const auto & species : mgd2.eqm_species_index)
1532 ASSERT_EQ(mgd2.eqm_species_transported[species.second], true);
1533 for (const auto & species : mgd2.kin_species_index)
1534 if (species.first == "Fe(OH)3(ppd)" || species.first == ">(s)FeO-")
1535 ASSERT_EQ(mgd2.kin_species_transported[species.second], false);
1536 else
1537 ASSERT_EQ(mgd2.kin_species_transported[species.second], true);
1538}
1539
1541TEST(PertinentGeochemicalSystemTest, redoxCapture)
1542{
1543 GeochemicalDatabaseReader database("database/moose_testdb.json");
1544
1545 PertinentGeochemicalSystem model_no_redox(
1546 database,
1547 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1548 {"Fe(OH)3(ppd)fake"},
1549 {"CH4(g)fake", "O2(g)"},
1550 {},
1551 {},
1552 {},
1553 "O2(aq)",
1554 "e-");
1555 ModelGeochemicalDatabase mgd_no_redox = model_no_redox.modelGeochemicalDatabase();
1556
1557 EXPECT_EQ(mgd_no_redox.redox_stoichiometry.m(), (unsigned)1);
1558 EXPECT_EQ(mgd_no_redox.redox_log10K.m(), (unsigned)1);
1559
1560 PertinentGeochemicalSystem model_redox(
1561 database,
1562 {"H2O", "H+", "HCO3-", "O2(aq)", "(O-phth)--", "CH4(aq)", "StoiCheckRedox", "Fe+++"},
1563 {"Fe(OH)3(ppd)fake"},
1564 {"CH4(g)fake", "O2(g)"},
1565 {},
1566 {},
1567 {},
1568 "O2(aq)",
1569 "e-");
1570 ModelGeochemicalDatabase mgd_redox = model_redox.modelGeochemicalDatabase();
1571
1572 EXPECT_EQ(mgd_redox.redox_lhs, "e-");
1573
1574 // StoiCheckRedox is not expressed in terms of O2(aq), and there is no Fe++ so Fe+++ does not
1575 // have a pair
1576 EXPECT_EQ(mgd_redox.redox_stoichiometry.m(), (unsigned)3);
1577 EXPECT_EQ(mgd_redox.redox_log10K.m(), (unsigned)3);
1578
1579 // not sure which order the redox has been ordered in. The reactions are:
1580 // e- = (1/4/7.5)(O-phth)-- + (1/2 + 5/4/7.5)H2O + (-1 - 6/4/7.5)H+ - 8/4/7.5HCO3-
1581 // e- = (1/8)CH4(aq) + (1/2 - 1/8)H2O - (1+1/8)H+ - (1/8)HCO3-
1582 const bool ophth_is_slot_one = (mgd_redox.redox_stoichiometry(1, 4) > 1.0E-6);
1583 const unsigned ophth_slot = (ophth_is_slot_one ? 1 : 2);
1584 const unsigned ch4_slot = (ophth_is_slot_one ? 2 : 1);
1585
1586 // e- = (1/4/7.5)(O-phth)-- + (1/2 + 5/4/7.5)H2O + (-1 - 6/4/7.5)H+ - 8/4/7.5HCO3-
1587 Real boa = 1.0 / 4.0 / 7.5;
1588 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 0), 0.5 + 5.0 * boa);
1589 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 1), -1 - 6.0 * boa);
1590 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 2), -8.0 * boa);
1591 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 3), 0.0);
1592 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 4), boa);
1593 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 5), 0.0);
1594 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 6), 0.0);
1595 EXPECT_EQ(mgd_redox.redox_stoichiometry(ophth_slot, 7), 0.0);
1596 EXPECT_NEAR(
1597 mgd_redox.redox_log10K(ophth_slot, 0), -boa * 594.3211 + 22.76135 - 0.25 * (-2.6610), 1E-8);
1598 EXPECT_NEAR(
1599 mgd_redox.redox_log10K(ophth_slot, 1), -boa * 542.8292 + 20.7757 - 0.25 * (-2.8990), 1E-8);
1600 EXPECT_NEAR(
1601 mgd_redox.redox_log10K(ophth_slot, 2), -boa * 482.3612 + 18.513025 - 0.25 * (-3.0580), 1E-8);
1602 EXPECT_NEAR(
1603 mgd_redox.redox_log10K(ophth_slot, 3), -boa * 425.9738 + 16.4658 - 0.25 * (-3.1250), 1E-8);
1604 EXPECT_NEAR(
1605 mgd_redox.redox_log10K(ophth_slot, 4), -boa * 368.7004 + 14.473225 - 0.25 * (-3.0630), 1E-8);
1606 EXPECT_NEAR(
1607 mgd_redox.redox_log10K(ophth_slot, 5), -boa * 321.8658 + 12.92125 - 0.25 * (-2.9140), 1E-8);
1608 EXPECT_NEAR(
1609 mgd_redox.redox_log10K(ophth_slot, 6), -boa * 281.8216 + 11.68165 - 0.25 * (-2.6600), 1E-8);
1610 EXPECT_NEAR(
1611 mgd_redox.redox_log10K(ophth_slot, 7), -boa * 246.4849 + 10.67105 - 0.25 * (-2.4100), 1E-8);
1612
1613 // e- = (1/8)CH4(aq) + (1/2 - 1/8)H2O - (1+1/8)H+ - (1/8)HCO3-
1614 boa = 1.0 / 8.0;
1615 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 0), 0.5 - boa);
1616 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 1), -1 - boa);
1617 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 2), -boa);
1618 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 3), 0.0);
1619 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 4), 0.0);
1620 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 5), boa);
1621 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 6), 0.0);
1622 EXPECT_EQ(mgd_redox.redox_stoichiometry(ch4_slot, 7), 0.0);
1623 EXPECT_NEAR(
1624 mgd_redox.redox_log10K(ch4_slot, 0), -boa * 157.8920 + 22.76135 - 0.25 * (-2.6610), 1E-8);
1625 EXPECT_NEAR(
1626 mgd_redox.redox_log10K(ch4_slot, 1), -boa * 144.1080 + 20.7757 - 0.25 * (-2.8990), 1E-8);
1627 EXPECT_NEAR(
1628 mgd_redox.redox_log10K(ch4_slot, 2), -boa * 127.9360 + 18.513025 - 0.25 * (-3.0580), 1E-8);
1629 EXPECT_NEAR(
1630 mgd_redox.redox_log10K(ch4_slot, 3), -boa * 112.8800 + 16.4658 - 0.25 * (-3.1250), 1E-8);
1631 EXPECT_NEAR(
1632 mgd_redox.redox_log10K(ch4_slot, 4), -boa * 97.7060 + 14.473225 - 0.25 * (-3.0630), 1E-8);
1633 EXPECT_NEAR(
1634 mgd_redox.redox_log10K(ch4_slot, 5), -boa * 85.2880 + 12.92125 - 0.25 * (-2.9140), 1E-8);
1635 EXPECT_NEAR(
1636 mgd_redox.redox_log10K(ch4_slot, 6), -boa * 74.7500 + 11.68165 - 0.25 * (-2.6600), 1E-8);
1637 EXPECT_NEAR(
1638 mgd_redox.redox_log10K(ch4_slot, 7), -boa * 65.6500 + 10.67105 - 0.25 * (-2.4100), 1E-8);
1639}
1640
1642TEST(PertinentGeochemicalSystemTest, redoxCapture_db_strange)
1643{
1644 GeochemicalDatabaseReader database("database/moose_testdb_e_strange.json");
1645
1646 PertinentGeochemicalSystem model_redox(
1647 database, {"H2O", "H+", "HCO3-", "O2(aq)", "(O-phth)--"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
1648 ModelGeochemicalDatabase mgd_redox = model_redox.modelGeochemicalDatabase();
1649
1650 EXPECT_EQ(mgd_redox.redox_lhs, "e-");
1651
1652 EXPECT_EQ(mgd_redox.redox_stoichiometry.m(), (unsigned)1);
1653 EXPECT_EQ(mgd_redox.redox_log10K.m(), (unsigned)1);
1654
1655 // Check the reaction:
1656 // e- = H2O + 3O2(aq) + OH- = 2H2O + 3O2(aq) - H+
1657 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 0), 2.0);
1658 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 1), -1.0);
1659 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 2), 0.0);
1660 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 3), 3.0);
1661 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 4), 0.0);
1662 EXPECT_NEAR(mgd_redox.redox_log10K(0, 0), 22.76135 + 14.9325, 1E-8);
1663 EXPECT_NEAR(mgd_redox.redox_log10K(0, 1), 20.7757 + 13.9868, 1E-8);
1664 EXPECT_NEAR(mgd_redox.redox_log10K(0, 2), 18.513025 + 13.0199, 1E-8);
1665 EXPECT_NEAR(mgd_redox.redox_log10K(0, 3), 16.4658 + 12.2403, 1E-8);
1666 EXPECT_NEAR(mgd_redox.redox_log10K(0, 4), 14.473225 + 11.5940, 1E-8);
1667 EXPECT_NEAR(mgd_redox.redox_log10K(0, 5), 12.92125 + 11.2191, 1E-8);
1668 EXPECT_NEAR(mgd_redox.redox_log10K(0, 6), 11.68165 + 11.0880, 1E-8);
1669 EXPECT_NEAR(mgd_redox.redox_log10K(0, 7), 10.67105 + 1001.2844, 1E-8);
1670}
1671
1673TEST(PertinentGeochemicalSystemTest, redoxCapture_redox_o_strange)
1674{
1675 GeochemicalDatabaseReader database("database/moose_testdb_e_strange.json");
1676
1677 PertinentGeochemicalSystem model_redox(
1678 database, {"H2O", "H+", "HCO3-", "O2(aq)", "(O-phth)_0"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
1679 ModelGeochemicalDatabase mgd_redox = model_redox.modelGeochemicalDatabase();
1680
1681 EXPECT_EQ(mgd_redox.redox_lhs, "e-");
1682
1683 EXPECT_EQ(mgd_redox.redox_stoichiometry.m(), (unsigned)1);
1684 EXPECT_EQ(mgd_redox.redox_log10K.m(), (unsigned)1);
1685
1686 // Check the reaction:
1687 // e- = H2O + 3O2(aq) + OH- = 2H2O + 3O2(aq) - H+
1688 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 0), 2.0);
1689 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 1), -1.0);
1690 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 2), 0.0);
1691 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 3), 3.0);
1692 EXPECT_EQ(mgd_redox.redox_stoichiometry(0, 4), 0.0);
1693 EXPECT_NEAR(mgd_redox.redox_log10K(0, 0), 22.76135 + 14.9325, 1E-8);
1694 EXPECT_NEAR(mgd_redox.redox_log10K(0, 1), 20.7757 + 13.9868, 1E-8);
1695 EXPECT_NEAR(mgd_redox.redox_log10K(0, 2), 18.513025 + 13.0199, 1E-8);
1696 EXPECT_NEAR(mgd_redox.redox_log10K(0, 3), 16.4658 + 12.2403, 1E-8);
1697 EXPECT_NEAR(mgd_redox.redox_log10K(0, 4), 14.473225 + 11.5940, 1E-8);
1698 EXPECT_NEAR(mgd_redox.redox_log10K(0, 5), 12.92125 + 11.2191, 1E-8);
1699 EXPECT_NEAR(mgd_redox.redox_log10K(0, 6), 11.68165 + 11.0880, 1E-8);
1700 EXPECT_NEAR(mgd_redox.redox_log10K(0, 7), 10.67105 + 1001.2844, 1E-8);
1701}
1702
1704TEST(PertinentGeochemicalSystemTest, addKineticRateExceptions)
1705{
1706 GeochemicalDatabaseReader database("database/moose_testdb.json");
1707 PertinentGeochemicalSystem model(database,
1708 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++"},
1709 {},
1710 {},
1711 {"Calcite"},
1712 {"CH4(aq)"},
1713 {},
1714 "O2(aq)",
1715 "e-");
1716
1717 try
1718 {
1719 KineticRateUserDescription rate("Ca++",
1720 1.0,
1721 2.0,
1722 true,
1723 0.0,
1724 0.0,
1725 0.0,
1726 {"H2O"},
1727 {3.0},
1728 {0.0},
1729 {0.0},
1730 4.0,
1731 5.0,
1732 6.0,
1733 7.0,
1734 DirectionChoiceEnum::BOTH,
1735 "H2O",
1736 0.0,
1737 -1.0,
1738 0.0);
1739 model.addKineticRate(rate);
1740 FAIL() << "Missing expected exception.";
1741 }
1742 catch (const std::exception & e)
1743 {
1744 std::string msg(e.what());
1745 ASSERT_TRUE(
1746 msg.find(
1747 "Cannot prescribe a kinetic rate to species Ca++ since it is not a kinetic species") !=
1748 std::string::npos)
1749 << "Failed with unexpected error message: " << msg;
1750 }
1751
1752 try
1753 {
1754 KineticRateUserDescription rate("CH4(aq)",
1755 1.0,
1756 2.0,
1757 true,
1758 0.0,
1759 0.0,
1760 0.0,
1761 {"H2O", "H++"},
1762 {3.0, 1.0},
1763 {0.0, 0.0},
1764 {0.0, 0.0},
1765 4.0,
1766 5.0,
1767 6.0,
1768 7.0,
1769 DirectionChoiceEnum::BOTH,
1770 "H2O",
1771 0.0,
1772 -1.0,
1773 0.0);
1774 model.addKineticRate(rate);
1775 FAIL() << "Missing expected exception.";
1776 }
1777 catch (const std::exception & e)
1778 {
1779 std::string msg(e.what());
1780 ASSERT_TRUE(msg.find("Promoting species H++ must be a basis or a secondary species") !=
1781 std::string::npos)
1782 << "Failed with unexpected error message: " << msg;
1783 }
1784
1785 try
1786 {
1787 KineticRateUserDescription rate("CH4(aq)",
1788 1.0,
1789 2.0,
1790 true,
1791 0.0,
1792 0.0,
1793 0.0,
1794 {},
1795 {},
1796 {},
1797 {},
1798 4.0,
1799 5.0,
1800 6.0,
1801 7.0,
1802 DirectionChoiceEnum::BOTH,
1803 "CH4(aq)",
1804 0.0,
1805 -1.0,
1806 0.0);
1807 model.addKineticRate(rate);
1808 FAIL() << "Missing expected exception.";
1809 }
1810 catch (const std::exception & e)
1811 {
1812 std::string msg(e.what());
1813 ASSERT_TRUE(msg.find("Progeny CH4(aq) must be a basis or a secondary species") !=
1814 std::string::npos)
1815 << "Failed with unexpected error message: " << msg;
1816 }
1817}
1818
1820TEST(PertinentGeochemicalSystemTest, addKineticRate)
1821{
1822 GeochemicalDatabaseReader database("database/moose_testdb.json");
1823 PertinentGeochemicalSystem model(database,
1824 {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++"},
1825 {},
1826 {},
1827 {"Calcite"},
1828 {"CH4(aq)"},
1829 {},
1830 "O2(aq)",
1831 "e-");
1832 KineticRateUserDescription rate("CH4(aq)",
1833 1.0,
1834 2.0,
1835 true,
1836 0.0,
1837 0.0,
1838 0.0,
1839 {"H2O", "OH-", "O2(aq)", "CO2(aq)", "CaCO3"},
1840 {3.0, 3.1, 3.2, 3.3, 3.4},
1841 {1.0, 2.0, 3.0, 4.0, 5.0},
1842 {1.25, 1.5, 1.75, 2.25, 3.25},
1843 4.0,
1844 5.0,
1845 6.0,
1846 7.0,
1847 DirectionChoiceEnum::BOTH,
1848 "H+",
1849 2.0,
1850 -1.0,
1851 0.0);
1852 model.addKineticRate(rate);
1853
1854 const ModelGeochemicalDatabase & mgd = model.modelGeochemicalDatabase();
1855
1856 EXPECT_EQ(mgd.kin_rate.size(), (std::size_t)1);
1857 EXPECT_EQ(mgd.kin_rate[0].kinetic_species_index, mgd.kin_species_index.at("CH4(aq)"));
1858 EXPECT_EQ(mgd.kin_rate[0].description.intrinsic_rate_constant, 1.0);
1859 EXPECT_EQ(mgd.kin_rate[0].description.area_quantity, 2.0);
1860 EXPECT_EQ(mgd.kin_rate[0].description.multiply_by_mass, true);
1861 std::vector<Real> pi_gold(mgd.basis_species_index.size() + mgd.eqm_species_index.size(), 0.0);
1862 std::vector<Real> pmi_gold(mgd.basis_species_index.size() + mgd.eqm_species_index.size(), 0.0);
1863 std::vector<Real> pmk_gold(mgd.basis_species_index.size() + mgd.eqm_species_index.size(), 0.0);
1864 EXPECT_EQ(mgd.kin_rate[0].promoting_indices.size(), pi_gold.size());
1865 EXPECT_EQ(mgd.kin_rate[0].promoting_monod_indices.size(), pmi_gold.size());
1866 EXPECT_EQ(mgd.kin_rate[0].promoting_half_saturation.size(), pmk_gold.size());
1867 pi_gold[0] = 3.0; // H2O
1868 pmi_gold[0] = 1.0;
1869 pmk_gold[0] = 1.25;
1870 pi_gold[5 + mgd.eqm_species_index.at("OH-")] = 3.1;
1871 pmi_gold[5 + mgd.eqm_species_index.at("OH-")] = 2.0;
1872 pmk_gold[5 + mgd.eqm_species_index.at("OH-")] = 1.5;
1873 pi_gold[3] = 3.2; // O2(aq)
1874 pmi_gold[3] = 3.0;
1875 pmk_gold[3] = 1.75;
1876 pi_gold[5 + mgd.eqm_species_index.at("CO2(aq)")] = 3.3;
1877 pmi_gold[5 + mgd.eqm_species_index.at("CO2(aq)")] = 4.0;
1878 pmk_gold[5 + mgd.eqm_species_index.at("CO2(aq)")] = 2.25;
1879 pi_gold[5 + mgd.eqm_species_index.at("CaCO3")] = 3.4;
1880 pmi_gold[5 + mgd.eqm_species_index.at("CaCO3")] = 5.0;
1881 pmk_gold[5 + mgd.eqm_species_index.at("CaCO3")] = 3.25;
1882 for (unsigned i = 0; i < pi_gold.size(); ++i)
1883 {
1884 EXPECT_EQ(mgd.kin_rate[0].promoting_indices[i], pi_gold[i]);
1885 EXPECT_EQ(mgd.kin_rate[0].promoting_monod_indices[i], pmi_gold[i]);
1886 EXPECT_EQ(mgd.kin_rate[0].promoting_half_saturation[i], pmk_gold[i]);
1887 }
1888 EXPECT_EQ(mgd.kin_rate[0].description.theta, 4.0);
1889 EXPECT_EQ(mgd.kin_rate[0].description.eta, 5.0);
1890 EXPECT_EQ(mgd.kin_rate[0].description.activation_energy, 6.0);
1891 EXPECT_EQ(mgd.kin_rate[0].description.one_over_T0, 7.0);
1892 EXPECT_EQ(mgd.kin_rate[0].progeny_index, mgd.basis_species_index.at("H+"));
1893 EXPECT_EQ(mgd.kin_rate[0].description.progeny, "H+");
1894 EXPECT_EQ(mgd.kin_rate[0].description.progeny_efficiency, 2.0);
1895
1896 KineticRateUserDescription ratec("Calcite",
1897 7.0,
1898 6.0,
1899 false,
1900 0.0,
1901 0.0,
1902 0.0,
1903 {"H+"},
1904 {-3.0},
1905 {-1.0},
1906 {-2.0},
1907 5.0,
1908 4.0,
1909 3.0,
1910 2.0,
1911 DirectionChoiceEnum::BOTH,
1912 "OH-",
1913 1.125,
1914 -1.0,
1915 0.0);
1916 model.addKineticRate(ratec);
1917
1918 EXPECT_EQ(mgd.kin_rate.size(), (std::size_t)2);
1919 EXPECT_EQ(mgd.kin_rate[1].kinetic_species_index, mgd.kin_species_index.at("Calcite"));
1920 EXPECT_EQ(mgd.kin_rate[1].description.intrinsic_rate_constant, 7.0);
1921 EXPECT_EQ(mgd.kin_rate[1].description.area_quantity, 6.0);
1922 EXPECT_EQ(mgd.kin_rate[1].description.multiply_by_mass, false);
1923 EXPECT_EQ(mgd.kin_rate[1].promoting_indices.size(), pi_gold.size());
1924 std::fill(pi_gold.begin(), pi_gold.end(), 0.0);
1925 std::fill(pmi_gold.begin(), pmi_gold.end(), 0.0);
1926 std::fill(pmk_gold.begin(), pmk_gold.end(), 0.0);
1927 pi_gold[1] = -3.0; // H++
1928 pmi_gold[1] = -1.0;
1929 pmk_gold[1] = -2.0;
1930 for (unsigned i = 0; i < pi_gold.size(); ++i)
1931 {
1932 EXPECT_EQ(mgd.kin_rate[1].promoting_indices[i], pi_gold[i]);
1933 EXPECT_EQ(mgd.kin_rate[1].promoting_monod_indices[i], pmi_gold[i]);
1934 EXPECT_EQ(mgd.kin_rate[1].promoting_half_saturation[i], pmk_gold[i]);
1935 }
1936 EXPECT_EQ(mgd.kin_rate[1].description.theta, 5.0);
1937 EXPECT_EQ(mgd.kin_rate[1].description.eta, 4.0);
1938 EXPECT_EQ(mgd.kin_rate[1].description.activation_energy, 3.0);
1939 EXPECT_EQ(mgd.kin_rate[1].description.one_over_T0, 2.0);
1940 EXPECT_EQ(mgd.kin_rate[1].progeny_index, 5 + mgd.eqm_species_index.at("OH-"));
1941 EXPECT_EQ(mgd.kin_rate[1].description.progeny, "OH-");
1942 EXPECT_EQ(mgd.kin_rate[1].description.progeny_efficiency, 1.125);
1943}
1944
1950TEST(PertinentGeochemicalSystemTest, kin_log10K1)
1951{
1952 GeochemicalDatabaseReader database("database/moose_testdb.json");
1953
1954 PertinentGeochemicalSystem model(database,
1955 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
1956 {},
1957 {"CH4(g)fake"},
1958 {"Fe(OH)3(ppd)fake"},
1959 {"(O-phth)--"},
1960 {">(s)FeO-"},
1961 "O2(aq)",
1962 "e-");
1963 const ModelGeochemicalDatabase & mgd = model.modelGeochemicalDatabase();
1964
1965 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 0),
1966 6.1946 + 2 * (-10.0553),
1967 eps);
1968 ASSERT_NEAR(
1969 mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 1), 4.8890 + 2 * (-8.4878), eps);
1970 ASSERT_NEAR(
1971 mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 2), 3.4608 + 2 * (-6.6954), eps);
1972 ASSERT_NEAR(
1973 mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 3), 2.2392 + 2 * (-5.0568), eps);
1974 ASSERT_NEAR(
1975 mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 4), 1.1150 + 2 * (-3.4154), eps);
1976 ASSERT_NEAR(
1977 mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 5), 0.2446 + 2 * (-2.0747), eps);
1978 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 6),
1979 -0.5504 + 2 * (-0.8908),
1980 eps);
1981 ASSERT_NEAR(
1982 mgd.kin_log10K(mgd.kin_species_index.at("Fe(OH)3(ppd)fake"), 7), -1.5398 + 2 * (0.2679), eps);
1983 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 0), 594.3211);
1984 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 1), 542.8292);
1985 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 2), 482.3612);
1986 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 3), 425.9738);
1987 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 4), 368.7004);
1988 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 5), 321.8658);
1989 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 6), 281.8216);
1990 EXPECT_EQ(mgd.kin_log10K(mgd.kin_species_index.at("(O-phth)--"), 7), 246.4849);
1991 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 0), 8.93, eps);
1992 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 1), 8.93 - 0.3 * (25 - 0), eps);
1993 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 2), 8.93 - 0.3 * (60 - 0), eps);
1994 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 3), 8.93 - 0.3 * (100 - 0), eps);
1995 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 4), 8.93 - 0.3 * (150 - 0), eps);
1996 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 5), 8.93 - 0.3 * (200 - 0), eps);
1997 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 6), 8.93 - 0.3 * (250 - 0), eps);
1998 ASSERT_NEAR(mgd.kin_log10K(mgd.kin_species_index.at(">(s)FeO-"), 7), 8.93 - 0.3 * (300 - 0), eps);
1999}
2000
2002TEST(PertinentGeochemicalSystemTest, initSwapToOrigBasis)
2003{
2004 GeochemicalDatabaseReader database("database/moose_testdb.json");
2005 PertinentGeochemicalSystem model(database, {"H2O", "H+"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
2006 ModelGeochemicalDatabase mgd = model.modelGeochemicalDatabase();
2007 ASSERT_EQ(mgd.swap_to_original_basis.n(), 0.0);
2008}
2009
2011TEST(PertinentGeochemicalSystemTest, getIndexOfOriginalBasisSpecies)
2012{
2013 GeochemicalDatabaseReader database("database/moose_testdb.json");
2014 PertinentGeochemicalSystem model(database, {"H2O", "H+"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
2015 try
2016 {
2017 model.getIndexOfOriginalBasisSpecies("OH-");
2018 FAIL() << "Missing expected exception.";
2019 }
2020 catch (const std::exception & e)
2021 {
2022 std::string msg(e.what());
2023 ASSERT_TRUE(msg.find("species OH- is not in the original basis") != std::string::npos)
2024 << "Failed with unexpected error message: " << msg;
2025 };
2026 EXPECT_EQ(model.getIndexOfOriginalBasisSpecies("H2O"), (unsigned)0);
2027 EXPECT_EQ(model.getIndexOfOriginalBasisSpecies("H+"), (unsigned)1);
2028}
2029
2031TEST(PertinentGeochemicalSystemTest, originalBasisNames)
2032{
2033 GeochemicalDatabaseReader database("database/moose_testdb.json");
2034 PertinentGeochemicalSystem model(database, {"H2O", "H+"}, {}, {}, {}, {}, {}, "O2(aq)", "e-");
2035 EXPECT_EQ(model.originalBasisNames()[0], "H2O");
2036 EXPECT_EQ(model.originalBasisNames()[1], "H+");
2037}
2038
2040TEST(PertinentGeochemicalSystemTest, allMinerals)
2041{
2042 GeochemicalDatabaseReader database("database/moose_testdb_all_minerals.json");
2043 PertinentGeochemicalSystem model(database,
2044 {"H2O", "H+", ">(s)FeOH", ">(w)FeOH", "Fe++", "HCO3-", "O2(aq)"},
2045 {"*"},
2046 {},
2047 {"Fe(OH)3(ppd)fake"},
2048 {"(O-phth)--"},
2049 {">(s)FeO-"},
2050 "O2(aq)",
2051 "e-");
2052 ModelGeochemicalDatabase mgd2 = model.modelGeochemicalDatabase();
2053
2054 for (const auto & species : mgd2.basis_species_index)
2055 ASSERT_EQ(mgd2.basis_species_mineral[species.second], false);
2056 EXPECT_EQ(mgd2.eqm_species_index.count("Calcite"), (std::size_t)0);
2057 EXPECT_EQ(mgd2.eqm_species_index.count("Calcite_asdf"), (std::size_t)0);
2058 EXPECT_EQ(mgd2.eqm_species_index.count("Fe(OH)3(ppd)fake"), (std::size_t)0);
2059 EXPECT_EQ(mgd2.eqm_species_index.count("Fe(OH)3(ppd)"), (std::size_t)1);
2060 EXPECT_EQ(mgd2.eqm_species_index.count("Goethite"), (std::size_t)1);
2061 EXPECT_EQ(mgd2.eqm_species_index.count("Something"), (std::size_t)1);
2062 for (const auto & species : mgd2.kin_species_index)
2063 if (species.first == "Fe(OH)3(ppd)fake")
2064 ASSERT_EQ(mgd2.kin_species_mineral[species.second], true);
2065 else
2066 ASSERT_EQ(mgd2.kin_species_mineral[species.second], false);
2067}
model
const PertinentGeochemicalSystem model(database, {"H2O", "H+", "HCO3-", "O2(aq)", "Ca++", ">(s)FeOH", "radius_neg1", "radius_neg1.5"}, {"Calcite"}, {}, {"Calcite_asdf"}, {"CH4(aq)"}, {">(s)FeOCa+"}, "O2(aq)", "e-")
database
const GeochemicalDatabaseReader database("database/moose_testdb.json", true, true, false)
mgd
const ModelGeochemicalDatabase mgd
Definition GeochemistryActivityCoefficientsDebyeHuckelTest.C:28
TEST
TEST(PertinentGeochemicalSystemTest, basisExceptions)
Test that:
Definition MinimalGeochemicalSystemTest.C:23
eps
const Real eps
Definition MinimalGeochemicalSystemTest.C:14
GeochemicalDatabaseReader
Class for reading geochemical reactions from a MOOSE geochemical database.
Definition GeochemicalDatabaseReader.h:216
GeochemicalDatabaseReader::getTemperatures
const std::vector< Real > & getTemperatures() const
Get the temperature points that the equilibrium constant is defined at.
Definition GeochemicalDatabaseReader.C:139
PertinentGeochemicalSystem
Constructs and stores a minimal amount of information that is pertinent to the user-defined geochemic...
Definition PertinentGeochemicalSystem.h:387
PertinentGeochemicalSystem::getIndexOfOriginalBasisSpecies
unsigned getIndexOfOriginalBasisSpecies(const std::string &name) const
Definition PertinentGeochemicalSystem.C:69
PertinentGeochemicalSystem::modelGeochemicalDatabase
const ModelGeochemicalDatabase & modelGeochemicalDatabase() const
Return a reference to the ModelGeochemicalDatabase structure.
Definition PertinentGeochemicalSystem.C:850
PertinentGeochemicalSystem::addKineticRate
void addKineticRate(const KineticRateUserDescription &description)
Adds a rate description for kinetic_species.
Definition PertinentGeochemicalSystem.C:856
PertinentGeochemicalSystem::originalBasisNames
std::vector< std::string > originalBasisNames() const
Definition PertinentGeochemicalSystem.C:86
libMesh::DenseMatrix::n
unsigned int n() const
libMesh::DenseMatrix::sub_matrix
DenseMatrix sub_matrix(unsigned int row_id, unsigned int row_size, unsigned int col_id, unsigned int col_size) const
KineticRateUserDescription
Holds a user-specified description of a kinetic rate.
Definition GeochemistryKineticRateCalculator.h:76
ModelGeochemicalDatabase
Data structure to hold all relevant information from the database file.
Definition PertinentGeochemicalSystem.h:102
ModelGeochemicalDatabase::eqm_species_mineral
std::vector< bool > eqm_species_mineral
eqm_species_mineral[i] = true iff the i^th equilibrium species is a mineral
Definition PertinentGeochemicalSystem.h:200
ModelGeochemicalDatabase::eqm_species_radius
std::vector< Real > eqm_species_radius
all quantities have an ionic radius (Angstrom) for computing activity (mineral radius = 0,...
Definition PertinentGeochemicalSystem.h:212
ModelGeochemicalDatabase::eqm_stoichiometry
DenseMatrix< Real > eqm_stoichiometry
eqm_stoichiometry(i, j) = stoichiometric coefficient for equilibrium species "i" in terms of the basi...
Definition PertinentGeochemicalSystem.h:224
ModelGeochemicalDatabase::basis_species_molecular_weight
std::vector< Real > basis_species_molecular_weight
all quantities have a molecular weight (g)
Definition PertinentGeochemicalSystem.h:183
ModelGeochemicalDatabase::kin_stoichiometry
DenseMatrix< Real > kin_stoichiometry
kin_stoichiometry(i, j) = stoichiometric coefficient for kinetic species "i" in terms of the basis sp...
Definition PertinentGeochemicalSystem.h:334
ModelGeochemicalDatabase::basis_species_radius
std::vector< Real > basis_species_radius
all quantities have an ionic radius (Angstrom) for computing activity (mineral radius = 0,...
Definition PertinentGeochemicalSystem.h:180
ModelGeochemicalDatabase::basis_species_charge
std::vector< Real > basis_species_charge
all quantities have a charge (mineral charge = 0, gas charge = 0, oxide charge = 0)
Definition PertinentGeochemicalSystem.h:177
ModelGeochemicalDatabase::eqm_species_molecular_volume
std::vector< Real > eqm_species_molecular_volume
all quantities have a molecular volume (cm^3) (only nonzero for minerals, however)
Definition PertinentGeochemicalSystem.h:218
ModelGeochemicalDatabase::eqm_species_molecular_weight
std::vector< Real > eqm_species_molecular_weight
all quantities have a molecular weight (g)
Definition PertinentGeochemicalSystem.h:215
ModelGeochemicalDatabase::basis_species_transported
std::vector< bool > basis_species_transported
basis_species_transported[j] = true iff the j^th basis species is transported in reactive-transport s...
Definition PertinentGeochemicalSystem.h:174
ModelGeochemicalDatabase::kin_species_name
std::vector< std::string > kin_species_name
kin_species_name[j] = name of the j^th kinetic species
Definition PertinentGeochemicalSystem.h:307
ModelGeochemicalDatabase::swap_to_original_basis
DenseMatrix< Real > swap_to_original_basis
Swap matrix that allows expression in terms of the original basis.
Definition PertinentGeochemicalSystem.h:371
ModelGeochemicalDatabase::basis_species_mineral
std::vector< bool > basis_species_mineral
basis_species_mineral[j] = true iff the j^th basis species is a mineral
Definition PertinentGeochemicalSystem.h:168
ModelGeochemicalDatabase::kin_rate
std::vector< KineticRateDefinition > kin_rate
rates given to kinetic species.
Definition PertinentGeochemicalSystem.h:341
ModelGeochemicalDatabase::kin_species_molecular_volume
std::vector< Real > kin_species_molecular_volume
all quantities have a molecular volume (cm^3/mol) (only nonzero for minerals, however)
Definition PertinentGeochemicalSystem.h:322
ModelGeochemicalDatabase::kin_log10K
DenseMatrix< Real > kin_log10K
kin_log10K(i, j) = log10(equilibrium constant for the i^th kinetic species at the j^th temperature po...
Definition PertinentGeochemicalSystem.h:328
ModelGeochemicalDatabase::basis_species_molecular_volume
std::vector< Real > basis_species_molecular_volume
all quantities have a molecular volume (cm^3) (only nonzero for minerals, however)
Definition PertinentGeochemicalSystem.h:186
ModelGeochemicalDatabase::eqm_species_index
std::unordered_map< std::string, unsigned > eqm_species_index
eqm_species_index[name] = index of the equilibrium species (secondary aqueous species,...
Definition PertinentGeochemicalSystem.h:194
ModelGeochemicalDatabase::original_database
const GeochemicalDatabaseReader * original_database
a pointer to the original database used to build this ModelGeochemicalDatabase
Definition PertinentGeochemicalSystem.h:156
ModelGeochemicalDatabase::basis_species_name
std::vector< std::string > basis_species_name
basis_species_name[j] = name of the j^th basis species
Definition PertinentGeochemicalSystem.h:165
ModelGeochemicalDatabase::kin_species_charge
std::vector< Real > kin_species_charge
all kinetic quantities have a charge (mineral charge = 0)
Definition PertinentGeochemicalSystem.h:316
ModelGeochemicalDatabase::basis_species_index
std::unordered_map< std::string, unsigned > basis_species_index
basis_species_index[name] = index of the basis species, within all ModelGeochemicalDatabase internal ...
Definition PertinentGeochemicalSystem.h:162
ModelGeochemicalDatabase::eqm_log10K
DenseMatrix< Real > eqm_log10K
eqm_log10K(i, j) = log10(equilibrium constant) for i^th equilibrium species at the j^th temperature p...
Definition PertinentGeochemicalSystem.h:230
ModelGeochemicalDatabase::basis_species_gas
std::vector< bool > basis_species_gas
basis_species_gas[j] = true iff the j^th basis species is a gas
Definition PertinentGeochemicalSystem.h:171
ModelGeochemicalDatabase::kin_species_index
std::unordered_map< std::string, unsigned > kin_species_index
kin_species_index[name] = index of the kinetic species, within all ModelGeochemicalDatabase internal ...
Definition PertinentGeochemicalSystem.h:304
ModelGeochemicalDatabase::eqm_species_name
std::vector< std::string > eqm_species_name
eqm_species_name[i] = name of the i^th eqm species
Definition PertinentGeochemicalSystem.h:197
ModelGeochemicalDatabase::eqm_species_charge
std::vector< Real > eqm_species_charge
all quantities have a charge (mineral charge = 0, gas charge = 0, oxide charge = 0)
Definition PertinentGeochemicalSystem.h:209
ModelGeochemicalDatabase::eqm_species_gas
std::vector< bool > eqm_species_gas
eqm_species_gas[i] = true iff the i^th equilibrium species is a gas
Definition PertinentGeochemicalSystem.h:203
ModelGeochemicalDatabase::kin_species_molecular_weight
std::vector< Real > kin_species_molecular_weight
all quantities have a molecular weight (g/mol)
Definition PertinentGeochemicalSystem.h:319
ModelGeochemicalDatabase::eqm_species_transported
std::vector< bool > eqm_species_transported
eqm_species_transported[i] = true iff the i^th eqm species is transported in reactive-transport sims
Definition PertinentGeochemicalSystem.h:206
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