12.2. Thermo Database¶
This section describes the general usage of RMG’s thermochemistry databases. Thermochemical data in RMG is reported using three different quantities:
Standard heat capacity data \(C_p^o(T)\) as a function of temperature \(T\)
Standard enthalpy of formation at 298K \(\Delta_fH^{o}(298K)\)
Standard entropy at 298K \(S^{o}(298K)\)
A heat capacity model based on the Wilhoit equation is used for inter- and extrapolation of the heat capacity data as a function of temperature.
12.2.1. Libraries¶
12.2.1.1. Library types¶
Two types of thermo libraries are available in RMG: “gas phase” and “liquid thermo” libraries respectively identified thanks to the absence or presence of the keyword solvent = “solvent_name” in the header of a thermo library. Here is an example of a liquid thermo library header:
name = "example_liquid_thermo_library"
solvent = "octane"
shortDesc = u"test"
longDesc = u"""
In this example the library name is “example_liquid_thermo_library” and thermo data provided was obtained in octane solvent. The only difference between gas phase and liquid phase thermo libraries is made through this keyword, the rest of the library is similar to gas phase.
Note
You can only provide one solvent per library and users should pay attention to not mix thermo of species obtained in different solvent in a same library. RMG will raise an error if users try to load a liquid thermo library obtained in another solvent that the one provided in input file. (in the example provided here, this liquid thermo library can only be used in liquid phase simulation with octane as solvent. RMG will also raise an error if user try to use liquid phase thermo library in gas phase simulations.
12.2.1.2. Species thermochemistry libraries¶
The folder RMG-database/input/thermo/libraries/ in RMG-database is the location to store
species thermochemistry libraries. Each particularly library is stored in a file
with the extension .py, e.g. ‘DFT_QCI_thermo.py’.
An example of a species thermochemistry entry is shown here below:
entry(
index = 1,
label = "H2",
molecule =
"""
1 H 0 0 {2,S}
2 H 0 0 {1,S}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([6.948,6.948,6.949,6.954,6.995,7.095,7.493],'cal/(mol*K)'),
H298 = (0,'kcal/mol'),
S298 = (31.095,'cal/(mol*K)'),
),
shortDesc = u"""""",
longDesc =
u"""
""",
)
The text above describes the first entry in the library (index = 1), labeled ‘H2’, through the adjacency list representation. Heat capacity data (‘Cpdata’) is described at 7 different temperatures, along with the standard enthalpy of formation at 298K (‘H298’), and the standard entropy at 298K (‘S298’).
According to the thermo classes availble in RMG, you can provide different thermo data: NASA, thermodata (as shown above), wilhoit or NASAPolynomial.
12.2.2. Groups¶
The folder RMG-database/input/thermo/groups/ in RMG-database is the location to store
group contribution databases. Each particularly type of group contribution is stored in a file
with the extension .py, e.g. ‘groups.py’:
file |
Type of group contribution |
|---|---|
gauche.py |
1,4-gauche non-nearest neighbor interactions (NNIs) |
group.py |
group additive values (GAVs) |
int15.py |
1,5-repulsion non-nearest neighbor interactions (NNIs) |
other.py |
other non-nearest neighbor interactions (NNIs) |
polycyclic.py |
polycyclic ring corrections (RSCs) |
radical.py |
hydrogen bond increments (HBIs) |
ring.py |
monocyclic ring corrections (RSCs) |
Like many other entities in RMG, the database of each type of group contribution is organized in a hierarchical tree, and is defined at the bottom of the database file. E.g.:
tree(
"""
L1: R
L2: C
L3: Cbf
L4: Cbf-CbCbCbf
L4: Cbf-CbCbfCbf
L4: Cbf-CbfCbfCbf
L3: Cb
L4: Cb-H
L4: Cb-Os
L4: Cb-S2s
L4: Cb-C
L5: Cb-Cs
L5: Cb-Cds
L6: Cb-(Cds-Od)
...
More information on hierarchical tree structures in RMG can be found here: Introduction.
12.2.2.1. Group additive values (GAV)¶
An example of a GAV entry in group.py is shown here below:
entry(
index = 3,
label = "Cbf-CbCbCbf",
group =
"""
1 * Cbf 0 {2,B} {3,B} {4,B}
2 Cb 0 {1,B}
3 Cb 0 {1,B}
4 Cbf 0 {1,B}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([3.01,3.68,4.2,4.61,5.2,5.7,6.2],'cal/(mol*K)',
'+|-', [0.1,0.1,0.1,0.1,0.1,0.1,0.1]),
H298 = (4.8,'kcal/mol','+|-',0.17),
S298 = (-5,'cal/(mol*K)','+|-',0.1),
),
shortDesc = u"""Cbf-CbfCbCb STEIN and FAHR; J. PHYS. CHEM. 1985, 89, 17, 3714""",
longDesc =
u"""
Taken from STEIN and FAHR; J. PHYS. CHEM. 1985, 89, 17, 3714
""",
)
The text above describes a GAV “Cbf-CbCbCbf”, with the central atom denoted by the asterisk in the adjacency list representation. Uncertainty margins are added in the data, after the unit specification. A short description ‘shortDesc’ specifies the origin of the data.
12.2.2.2. Ring Strain Corrections (RSC)¶
RMG distinguishes between monocyclic and polycyclic ring correction databases.
Monocyclic RSCs are used for molecules that contain one single ring. An example of a monocyclic RSC entry in ring.py is shown here below:
entry(
index = 1,
label = "Cyclopropane",
group =
"""
1 * Cs 0 {2,S} {3,S}
2 Cs 0 {1,S} {3,S}
3 Cs 0 {1,S} {2,S}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([-3.227,-2.849,-2.536,-2.35,-2.191,-2.111,-1.76],'cal/(mol*K)'),
H298 = (27.53,'kcal/mol'),
S298 = (32.0088,'cal/(mol*K)'),
),
shortDesc = u"""Cyclopropane ring BENSON""",
longDesc =
u"""
""",
)
A molecule may have two or more fused rings that mutually interact. In that case, a polycyclic ring strain correction may be more adequate. RMG identifies molecules with fused ring systems and subsequently searches through polycyclic.py to identify an adequate RSC.
An example of a polycyclic RSC entry in polycyclic.py is shown here below:
entry(
index = 2,
label = "norbornane",
group =
"""
1 * Cs 0 {3,S} {4,S} {7,S}
2 Cs 0 {3,S} {5,S} {6,S}
3 Cs 0 {1,S} {2,S}
4 Cs 0 {1,S} {5,S}
5 Cs 0 {2,S} {4,S}
6 Cs 0 {2,S} {7,S}
7 Cs 0 {1,S} {6,S}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([-4.5,-3.942,-3.291,-2.759,-2.08,-1.628,-0.898],'cal/(mol*K)'),
H298 = (16.14,'kcal/mol'),
S298 = (53.47,'cal/(mol*K)'),
),
shortDesc = u"""""",
longDesc =
u"""
""",
)
12.2.2.3. Hydrogen Bond Increments (HBI)¶
An example of a HBI entry in radical.py is shown here below:
entry(
index = 4,
label = "CH3",
group =
"""
1 * C 1 {2,S} {3,S} {4,S}
2 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([0.71,0.34,-0.33,-1.07,-2.43,-3.54,-5.43],'cal/(mol*K)'),
H298 = (104.81,'kcal/mol','+|-',0.1),
S298 = (0.52,'cal/(mol*K)'),
),
shortDesc = u"""Calculated in relation to methane from NIST values""",
longDesc =
u"""
""",
)
12.2.2.4. Non-nearest neighbor interactions¶
The majority of the NNIs groups pertain to small enthalpy of formation corrections. Only a very limited number include entropy or heat capacity corrections. The database other.py contains cis-, ortho- and ketene-corrections.
An example of a NNI entry in gauche.py is shown here below:
entry(
index = 11,
label = "Cs(Cs(CsCsR)Cs(CsCsR)RR)",
group =
"""
1 * Cs 0 {2,S} {3,S} {4,S} {5,S}
2 Cs 0 {1,S} {6,S} {7,S} {8,S}
3 Cs 0 {1,S} {9,S} {10,S} {11,S}
4 {Cd,Cdd,Ct,Cb,Cbf,Os,CO,H} 0 {1,S}
5 {Cd,Cdd,Ct,Cb,Cbf,Os,CO,H} 0 {1,S}
6 Cs 0 {2,S}
7 Cs 0 {2,S}
8 {Cd,Cdd,Ct,Cb,Cbf,Os,CO,H} 0 {2,S}
9 Cs 0 {3,S}
10 Cs 0 {3,S}
11 {Cd,Cdd,Ct,Cb,Cbf,Os,CO,H} 0 {3,S}
""",
thermo = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],'K'),
Cpdata = ([0,0,0,0,0,0,0],'cal/(mol*K)'),
H298 = (0.8,'kcal/mol'),
S298 = (0,'cal/(mol*K)'),
),
shortDesc = u"""""",
longDesc =
u"""
""",
)
