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specmicp/tests/specmicp_database/database_species.cpp
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database_species.cpp
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#include "catch.hpp"
#include "specmicp_database/species/species.hpp"
#include "specmicp_database/species/component_list.hpp"
#include "specmicp_database/species/aqueous_list.hpp"
#include "specmicp_database/species/mineral_list.hpp"
#include <iostream>
using namespace specmicp;
using namespace specmicp::database;
TEST_CASE("WrapperSpecies") {
SECTION("VectorSpeciesWrapper") {
VectorSpeciesWrapper wrap(3);
wrap.set_value(0, 1);
wrap.set_value(1, 2);
wrap.set_value(2, 3);
CHECK(wrap(0) == 1);
CHECK(wrap.get_value(1) == 2);
wrap.move_erase(2, 1);
wrap.resize(2);
CHECK(wrap(1) == 3);
Vector other(2);
other << 1, 3;
CHECK(wrap.dot(other) == 10);
Matrix transformation(2, 2);
transformation << 1, 0, 0, 1;
wrap.transform(transformation);
CHECK(wrap(0) == 1);
CHECK(wrap(1) == 3);
transformation << 2, 1, 0, 3;
wrap.transform(transformation);
CHECK(wrap(0) == 5);
CHECK(wrap(1) == 9);
}
SECTION("MatrixSpeciesWrapper") {
MatrixSpeciesWrapper wrap(3, 2);
CHECK(wrap.size() == 3);
wrap.set_value(0, 0, 1);
wrap.set_value(0, 1, 2);
wrap.set_value(1, 0, 3);
CHECK(wrap(1, 1) == 0);
CHECK(wrap(0, 1) == 2);
wrap.move_erase(1, 0);
wrap.resize(1);
CHECK(wrap.size() == 1);
CHECK(wrap(0, 0) == 3);
}
}
TEST_CASE("DatabaseSpecies", "[Species]")
{
SECTION("SpeciesList")
{
SpeciesList species_list(2);
CHECK(species_list.is_valid() == false);
REQUIRE(species_list.size() == 2);
species_list.set_label(0, "HOP");
species_list.set_label(1, "REHOP");
species_list.set_valid();
REQUIRE(species_list.size() == 2);
CHECK(species_list.is_valid() == true);
CHECK(species_list.get_label(0) == "HOP");
CHECK(species_list.get_label(1) == "REHOP");
CHECK(species_list.get_id("HOP") == 0);
CHECK(species_list.get_id("REHOP") == 1);
CHECK(species_list.get_id("OUHLALA") == no_species);
species_list.move_erase(1, 0);
CHECK(species_list.is_valid() == false);
species_list.resize(1);
species_list.set_valid();
REQUIRE(species_list.size() == 1);
CHECK(species_list.get_label(0) == "REHOP");
CHECK(species_list.get_id("HOP") == no_species);
CHECK(species_list.get_id("REHOP") == 0);
CHECK(species_list.get_id("OUHLALA") == no_species);
CHECK(species_list.is_valid() == true);
}
SECTION("ReactiveSpeciesList") {
ReactiveSpeciesList slist(3, 3);
slist.set_label(0, "S1");
slist.set_nu_ji(0, 0, 1);
slist.set_nu_ji(0, 1, 2);
slist.set_nu_ji(0, 2, 3);
slist.set_logk(0, -1);
slist.set_label(1, "S2");
slist.set_nu_ji(1, 0, 4);
slist.set_nu_ji(1, 1, 5);
slist.set_logk(1, -2);
slist.set_label(2, "S3");
slist.set_nu_ji(2, 0, 6);
slist.set_nu_ji(2, 2, 7);
slist.set_logk(2, -3);
CHECK(slist.is_valid() == false);
slist.set_valid();
CHECK(slist.is_valid() == true);
CHECK(slist.size() == 3);
CHECK(slist.get_id("S3") == 2);
CHECK(slist.get_label(1) == "S2");
CHECK(slist.nu_ji(2, 0) == 6);
CHECK(slist.nu_ji(1, 1) == 5);
// check default value
CHECK(slist.nu_ji(1, 2) == 0);
CHECK(slist.nu_ji(0, 2) == 3);
slist.move_erase(2, 1);
slist.resize(2);
CHECK(slist.is_valid() == false);
slist.set_valid();
CHECK(slist.is_valid() == true);
CHECK(slist.size() == 2);
CHECK(slist.get_label(0) == "S1");
CHECK(slist.get_label(1) == "S3");
CHECK(slist.get_id("S2") == no_species);
CHECK(slist.nu_ji(1, 0) == 6);
CHECK(slist.logk(1) == -3);
}
}
TEST_CASE("ComponentList", "[database,species,component]") {
ComponentList clist(3);
clist.set_values(0, {"C1", 1.0, IonicModelValues{0, 1, 2}});
clist.set_values(1, {"C2", 2.0, IonicModelValues{-1, 1, 2}});
clist.set_values(2, {"C3", 3.0, IonicModelValues{2, 3, 4}});
SECTION("Initialization") {
CHECK(clist.get_label(1) == "C2");
CHECK(clist.get_id("C3") == 2);
CHECK(clist.get_id("NotHere") == -1);
CHECK(clist.molar_mass(1) == 2.0);
CHECK(clist.charge(0) == 0.0);
CHECK(clist.charge(1) == -1.0);
CHECK(clist.a_debye(2) == 3.0);
CHECK(clist.b_debye(2) == 4.0);
}
SECTION("Move and erase") {
clist.move_erase(2, 1);
CHECK(clist.molar_mass(1) == 3.0);
CHECK(clist.get_label(1) == "C3");
CHECK(clist.get_id("C2") == no_species);
CHECK(clist.charge(0) == 0.0);
CHECK(clist.charge(1) == 2.0);
CHECK(clist.a_debye(1) == 3.0);
CHECK(clist.b_debye(1) == 4.0);
}
SECTION("Molar mass wrapper") {
Vector stoech(3);
stoech << 1.0, 2.0, 3.0;
auto molmass = clist.molar_mass_compounds(stoech);
CHECK(molmass == 14.0);
}
}
TEST_CASE("AqueousList", "[database,species,aqueous]") {
AqueousList alist(3,2);
alist.set_values(0, {"A1", -1, IonicModelValues{1, 2, 3}});
alist.set_values(1, {"A2", -2, IonicModelValues{4, 5, 6}});
alist.set_values(2, {"A3", -3, IonicModelValues{7, 8, 9}});
alist.set_nu_ji(0, 0, 1);
alist.set_nu_ji(0, 1, 2);
alist.set_nu_ji(1, 0, 3);
alist.set_nu_ji(1, 1, 4);
alist.set_nu_ji(2, 0, 5);
SECTION("Initialisation") {
REQUIRE(alist.size() == 3);
CHECK(alist.get_label(1) == "A2");
CHECK(alist.get_id("A3") == 2);
CHECK(alist.get_id("NotHere") == -1);
CHECK(alist.logk(0) == -1);
CHECK(alist.logk(1) == -2);
CHECK(alist.logk(2) == -3);
CHECK(alist.nu_ji(0, 0) == 1);
CHECK(alist.nu_ji(0, 1) == 2);
CHECK(alist.nu_ji(1, 0) == 3);
CHECK(alist.nu_ji(1, 1) == 4);
CHECK(alist.nu_ji(2, 0) == 5);
CHECK(alist.nu_ji(2, 1) == 0);
}
SECTION("Move erase") {
alist.move_erase(2, 1);
alist.resize(2);
CHECK(alist.size() == 2);
CHECK(alist.get_id("A3") == 1);
CHECK(alist.get_id("A2") == -1);
CHECK(alist.logk(1) == -3);
CHECK(alist.nu_ji(1, 0) == 5);
CHECK(alist.nu_ji(1, 1) == 0);
}
SECTION("Canonicalization") {
alist.canonicalize(2, 1, 1.0);
CHECK(alist.nu_ji(2, 0) == 8.0);
CHECK(alist.nu_ji(2, 1) == 4.0);
CHECK(alist.logk(2) == -5.0);
}
}
TEST_CASE("MineralList", "[Minerals,species]") {
MineralList mlist(3, 3);
mlist.set_values(0, {"M1", -1.0, 10.0});
mlist.set_values(1, {"M2", -2.0, 20.0});
mlist.set_values(2, {"M3", -3.0, 30.0});
Matrix stoech_coefficient(3, 3);
stoech_coefficient <<
1, 2, 3,
4, 5, 6,
7, 8, 9;
mlist.set_nu_matrix(stoech_coefficient);
mlist.set_valid();
SECTION("Initialization") {
CHECK(mlist.is_valid() == true);
CHECK(mlist.get_label(2) == "M3");
CHECK(mlist.get_id("M2") == 1);
CHECK(mlist.get_id("NotHere") == no_species);
CHECK(mlist.nu_ji(2, 2) == 9);
CHECK(mlist.nu_ji(1, 2) == 6);
CHECK(mlist.logk(2) == -3);
CHECK(mlist.logk(1) == -2);
CHECK(mlist.molar_volume(0) == 10.0);
CHECK(mlist.molar_volume(1) == 20.0);
}
SECTION("Move Erase") {
mlist.move_erase(2, 1);
CHECK(mlist.is_valid() == false);
mlist.resize(2);
mlist.set_valid();
CHECK(mlist.is_valid() == true);
CHECK(mlist.nu_ji(1, 2) == 9);
CHECK(mlist.logk(1) == -3);
CHECK(mlist.logk(0) == -1);
CHECK(mlist.molar_volume(0) == 10.0);
CHECK(mlist.molar_volume(1) == 30.0);
}
SECTION("Move erase to") {
MineralList mlist2(3, 3);
mlist2.set_values(0, {"MK1", -4.0, 40.0});
mlist2.set_values(1, {"MK2", -5.0, 50.0});
mlist2.set_values(2, {"MK3", -6.0, 60.0});
Matrix stoech_coefficient2(3, 3);
stoech_coefficient2 <<
-1, -2, -3,
-4, -5, -6,
-7, -8, -9;
mlist2.set_nu_matrix(stoech_coefficient2);
mlist2.set_valid();
mlist2.resize(4);
mlist.move_erase_to(2, mlist2, 3);
mlist.resize(2);
CHECK(mlist.is_valid() == false);
CHECK(mlist2.is_valid() == false);
mlist.set_valid();
mlist2.set_valid();
CHECK(mlist.is_valid() == true);
CHECK(mlist2.is_valid() == true);
CHECK(mlist.size() == 2);
CHECK(mlist2.size() == 4);
CHECK(mlist2.get_id("M3") == 3);
CHECK(mlist.get_id("M3") == no_species);
CHECK(mlist2.nu_ji(3, 2) == 9);
CHECK(mlist2.molar_volume(3) == 30);
CHECK(mlist2.logk(3) == -3);
}
SECTION("Canonicalization") {
AqueousList alist(3,3);
alist.set_values(0, {"A1", -1.0, IonicModelValues{1, 2, 3}});
alist.set_values(1, {"A2", -2.0, IonicModelValues{4, 5, 6}});
alist.set_values(2, {"A3", -3.0, IonicModelValues{7, 8, 9}});
Matrix acoeff(3, 3);
acoeff << 0, 1, 2,
3, 4, 5,
6, 7, 8;
alist.set_nu_matrix(acoeff);
mlist.canonicalize(0, alist, 0, 1.0);
CHECK(mlist.nu_ji(0, 0) == 1.0);
CHECK(mlist.nu_ji(0, 1) == 3.0);
CHECK(mlist.nu_ji(0, 2) == 5.0);
CHECK(mlist.logk(0) == -2.0);
mlist.canonicalize(1, alist, 1, -2.0);
CHECK(mlist.nu_ji(1, 0) == 4.0-2*3.0);
CHECK(mlist.nu_ji(1, 1) == 5.0-2*4.0);
CHECK(mlist.nu_ji(1, 2) == 6.0-2*5.0);
CHECK(mlist.logk(1) == -2.0+2.0*2.0);
}
}
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