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database_reader.cpp
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Created
Wed, Jun 26, 17:35
Size
6 KB
Mime Type
text/x-c
Expires
Fri, Jun 28, 17:35 (2 d)
Engine
blob
Format
Raw Data
Handle
18556171
Attached To
rSPECMICP SpecMiCP / ReactMiCP
database_reader.cpp
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#include "catch.hpp"
#include "database/reader_common.hpp"
#include "database/yaml_reader.hpp"
#include <string>
#include <istream>
#include <sstream>
#include "str_database.hpp"
using
namespace
specmicp
;
using
namespace
specmicp
::
database
;
#include "utils/timer.hpp"
#include <iostream>
TEST_CASE
(
"Database reader - help function"
)
{
SECTION
(
"Equation Parsing"
)
{
std
::
map
<
std
::
string
,
specmicp
::
scalar_t
>
compo
;
std
::
string
eq
=
"A, 2 B, -C, -3D, SDF, - 3 de, - X"
;
specmicp
::
database
::
parse_equation
(
eq
,
compo
);
CHECK
(
compo
[
"A"
]
==
1
);
CHECK
(
compo
[
"B"
]
==
2
);
CHECK
(
compo
[
"C"
]
==
-
1
);
CHECK
(
compo
[
"D"
]
==
-
3
);
CHECK
(
compo
[
"SDF"
]
==
1
);
CHECK
(
compo
[
"de"
]
==
-
3
);
CHECK
(
compo
[
"X"
]
==
-
1
);
}
SECTION
(
"Charge parsing"
)
{
CHECK
(
specmicp
::
database
::
charge_from_label
(
"neutral"
)
==
0
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"neutral[]"
)
==
0
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[+]"
)
==
1
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[-]"
)
==
-
1
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[2]"
)
==
2
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[2-]"
)
==
-
2
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[2+]"
)
==
+
2
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[-3]"
)
==
-
3
);
CHECK
(
specmicp
::
database
::
charge_from_label
(
"charge[+1]"
)
==
+
1
);
CHECK_THROWS_AS
(
specmicp
::
database
::
charge_from_label
(
"charge[+3"
),
specmicp
::
database
::
db_invalid_syntax
);
CHECK_THROWS_AS
(
specmicp
::
database
::
charge_from_label
(
"charge[ddd]"
),
specmicp
::
database
::
db_invalid_syntax
);
}
}
TEST_CASE
(
"Database reader"
)
{
SECTION
(
"Good database"
)
{
Timer
timer
;
std
::
istringstream
input
(
good_test_database
);
DataReaderYaml
reader
(
input
);
RawDatabasePtr
data
=
reader
.
get_database
();
timer
.
stop
();
std
::
cout
<<
"Reading database : "
<<
timer
.
elapsed_time
()
*
1000
<<
" ms (Ref 0.20ms)"
<<
std
::
endl
;
CHECK
(
data
->
aqueous
.
is_valid
());
CHECK
(
data
->
components
.
is_valid
());
CHECK
(
data
->
minerals
.
is_valid
());
CHECK
(
data
->
minerals_kinetic
.
is_valid
());
CHECK
(
data
->
gas
.
is_valid
());
CHECK
(
data
->
is_valid
());
size_t
hash
=
data
->
get_hash
();
// component
// =========
CHECK
(
data
->
nb_component
()
==
5
);
CHECK
(
data
->
components
.
get_id
(
"C1[-]"
)
==
2
);
CHECK
(
data
->
components
.
get_label
(
0
)
==
"H2O"
);
CHECK
(
data
->
components
.
charge
(
1
)
==
-
1
);
CHECK
(
data
->
a_debye_component
(
2
)
==
1.0
);
CHECK
(
data
->
b_debye_component
(
3
)
==
0.4
);
// aqueous
// =======
CHECK
(
data
->
nb_aqueous
()
==
3
);
CHECK
(
data
->
aqueous
.
get_id
(
"A2"
)
==
-
1
);
// normal
// ------
CHECK
(
data
->
nu_aqueous
(
0
,
0
)
==
0.0
);
CHECK
(
data
->
nu_aqueous
(
0
,
1
)
==
0.0
);
CHECK
(
data
->
nu_aqueous
(
0
,
2
)
==
1.0
);
CHECK
(
data
->
nu_aqueous
(
0
,
3
)
==
1.0
);
CHECK
(
data
->
nu_aqueous
(
0
,
4
)
==
0.0
);
CHECK
(
data
->
logk_aqueous
(
0
)
==
-
2.0
);
// canonicalization
// ----------------
CHECK
(
data
->
nu_aqueous
(
1
,
0
)
==
0.0
);
CHECK
(
data
->
nu_aqueous
(
1
,
1
)
==
0.0
);
CHECK
(
data
->
nu_aqueous
(
1
,
2
)
==
1.0
);
CHECK
(
data
->
nu_aqueous
(
1
,
3
)
==
2.0
);
CHECK
(
data
->
nu_aqueous
(
1
,
4
)
==
0.0
);
CHECK
(
data
->
logk_aqueous
(
1
)
==
-
4
);
// aqueous parameters
// ------------------
CHECK
(
data
->
charge_aqueous
(
0
)
==
0
);
CHECK
(
data
->
charge_aqueous
(
1
)
==
+
1
);
CHECK
(
data
->
a_debye_aqueous
(
1
)
==
1.0
);
CHECK
(
data
->
b_debye_aqueous
(
1
)
==
0.4
);
// Minerals
// ========
CHECK
(
data
->
nb_mineral
()
==
2
);
CHECK
(
data
->
minerals
.
get_label
(
0
)
==
"M1"
);
CHECK
(
data
->
minerals
.
get_label
(
1
)
==
"M2"
);
CHECK
(
data
->
nu_mineral
(
0
,
0
)
==
0.0
);
CHECK
(
data
->
nu_mineral
(
0
,
1
)
==
0.0
);
CHECK
(
data
->
nu_mineral
(
0
,
2
)
==
1.0
);
CHECK
(
data
->
nu_mineral
(
0
,
3
)
==
1.0
);
CHECK
(
data
->
nu_mineral
(
0
,
4
)
==
0.0
);
CHECK
(
data
->
logk_mineral
(
0
)
==
-
7
);
CHECK
(
data
->
molar_volume_mineral
(
0
)
==
1e-6
*
10.0
);
CHECK
(
data
->
molar_mass_mineral
(
0
,
units
::
MassUnit
::
gram
)
==
5.0
);
CHECK
(
data
->
nu_mineral
(
1
,
0
)
==
0.0
);
CHECK
(
data
->
nu_mineral
(
1
,
1
)
==
0.0
);
CHECK
(
data
->
nu_mineral
(
1
,
2
)
==
2.0
);
CHECK
(
data
->
nu_mineral
(
1
,
3
)
==
2.0
);
CHECK
(
data
->
nu_mineral
(
1
,
4
)
==
1.0
);
CHECK
(
data
->
logk_mineral
(
1
)
==
-
6
+
data
->
logk_aqueous
(
1
)
+
data
->
logk_aqueous
(
2
));
CHECK
(
data
->
unsafe_molar_volume_mineral
(
1
)
<
0
);
CHECK_THROWS
(
data
->
molar_volume_mineral
(
1
));
// Kinetic Minerals
// ================
CHECK
(
data
->
nb_mineral_kinetic
()
==
1
);
CHECK
(
data
->
minerals_kinetic
.
get_label
(
0
)
==
"MK1"
);
CHECK
(
data
->
nu_mineral_kinetic
(
0
,
0
)
==
0.0
);
CHECK
(
data
->
nu_mineral_kinetic
(
0
,
1
)
==
0.0
);
CHECK
(
data
->
nu_mineral_kinetic
(
0
,
2
)
==
1.0
);
CHECK
(
data
->
nu_mineral_kinetic
(
0
,
3
)
==
1.0
);
CHECK
(
data
->
nu_mineral_kinetic
(
0
,
4
)
==
2.0
);
CHECK
(
data
->
logk_mineral_kinetic
(
0
)
==
-
9
);
CHECK
(
data
->
molar_volume_mineral_kinetic
(
0
)
==
1e-6
*
30.0
);
CHECK
(
data
->
molar_mass_mineral_kinetic
(
0
,
units
::
MassUnit
::
gram
)
==
13.0
);
// Gas
// ======
CHECK
(
data
->
nb_gas
()
==
1
);
CHECK
(
data
->
gas
.
get_label
(
0
)
==
"G1"
);
CHECK
(
data
->
nu_gas
(
0
,
0
)
==
0.0
);
CHECK
(
data
->
nu_gas
(
0
,
1
)
==
0.0
);
CHECK
(
data
->
nu_gas
(
0
,
2
)
==
0.0
);
CHECK
(
data
->
nu_gas
(
0
,
3
)
==
0.0
);
CHECK
(
data
->
nu_gas
(
0
,
4
)
==
1.0
);
CHECK
(
data
->
logk_gas
(
0
)
==
3.0
);
// sorbed
// ======
CHECK
(
data
->
nb_sorbed
()
==
1
);
CHECK
(
data
->
sorbed
.
get_label
(
0
)
==
"S1"
);
CHECK
(
data
->
nu_sorbed
(
0
,
0
)
==
0.0
);
CHECK
(
data
->
nu_sorbed
(
0
,
1
)
==
0.0
);
CHECK
(
data
->
nu_sorbed
(
0
,
2
)
==
0.0
);
CHECK
(
data
->
nu_sorbed
(
0
,
3
)
==
0.0
);
CHECK
(
data
->
nu_sorbed
(
0
,
4
)
==
1.0
);
CHECK
(
data
->
logk_sorbed
(
0
)
==
-
6
);
// Compounds
// =========
CHECK
(
data
->
nb_compounds
()
==
1
);
CHECK
(
data
->
get_label_compound
(
0
)
==
"Comp1"
);
CHECK
(
data
->
nu_compound
(
0
,
0
)
==
2.0
);
CHECK
(
data
->
nu_compound
(
0
,
1
)
==
0.0
);
CHECK
(
data
->
nu_compound
(
0
,
2
)
==
0.0
);
CHECK
(
data
->
nu_compound
(
0
,
3
)
==
0.0
);
CHECK
(
data
->
nu_compound
(
0
,
4
)
==
1.0
);
// Elements
// =========
CHECK
(
data
->
get_id_component_from_element
(
"plop"
)
==
-
1
);
CHECK
(
data
->
get_id_component_from_element
(
"C1"
)
!=
-
1
);
CHECK
(
data
->
get_label_component_from_element
(
"C1"
)
==
"C1[-]"
);
CHECK
(
data
->
get_label_component_from_element
(
"C3"
)
==
"C3"
);
//
data
->
freeze_db
();
CHECK
(
data
->
get_hash
()
==
hash
);
CHECK
(
data
->
is_valid
());
}
}
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