Dear Prof. David,
To some organic molecules, for example sec-Butanol, when I simulate the adsorption in some zeolites, the excess adsorption is nan +/- or negative values. Therefore, the "nan +/-" or "negative value" excess adsorption mean none?
Looking forward to your reply!
Best wishes!
The followings is the definition of sec-Butanol, which is with the referrence of ethanol and alkane.
#critical constants:Temperature[T], Pressure[Pa], and Acentric factor[-]
0.0
0.0
0.0
#number of atoms
6
#number of group
1
#alkane-group
flexible
#number of atoms
6
#atomic positions
0 CH3_sp3
1 CH_alc
2 O_alc
3 H_alc
4 CH2_sp3
5 CH3_sp3
#chiral centers Bond Bonddipoles Bend UrayBradley Invbend Torsion Imp. Torsion Bond/Bond Stretrch/Bend Bend/bend Stetrch/Torsion
0 5 0 5 0 0 4 0 0 0 0 0
#Bond stretch: atom n1-n2, type, parameters
0 1 FIXED_BOND 1.535
1 2 FIXED_BOND 1.430
2 3 FIXED_BOND 0.945
1 4 FIXED_BOND 1.535
4 5 HARMONIC_BOND 96500 1.535
#Bond bending: atom n1-n2-n3, type, parameters
0 1 2 HARMONIC_BEND 50400 109.47
0 1 4 HARMONIC_BEND 62500 112
1 2 3 HARMONIC_BEND 55400 108.5
4 1 2 HARMONIC_BEND 50400 109.47
5 4 1 HARMONIC_BEND 62500 114
#Torsion n1-n2-n3-n4 type
0 1 2 3 TRAPPE_DIHEDRAL 0.0 209.82 -29.17 187.93
4 1 2 3 TRAPPE_DIHEDRAL 0.0 209.82 -29.17 187.93
0 1 4 5 TRAPPE_DIHEDRAL 0.0 335.03 -68.19 791.32
5 4 1 2 TRAPPE_DIHEDRAL -106.68 176.62 -53.34 769.93
#number of config moves
0
The computation of excess adorption is done using an equation of state (Peng-Robinson), which requires that you specify the critical constants for your molecule (at the top of the molecule definition).
Dear Prof. David,
Thanks for your reply.
In the simulation of oraganic adsorption, without knowing the critical constants of the organic molecules (sec-Butanol), and I set the fugacity coefficent as 1.0. In the output file, it shows that the execess adsorption is "nan +/-". So, is there any wrong about my operation?
Thanks very much!
Best wishes!
No, there is nothing wrong. With the fugacity coefficient specified as 1.0, the code will not compute the excess adsorption. For that it needs to use an equation of state using the critical constants.
Note that you can also trivially compute excess adsorption from absolute adsorption by hand (see literature).
Dear Professor David,
I am a beginner of RAPSA, and want to ask some thing about the definition of molecule.
take C7 as an example.
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
540.13
2736000.0
0.349
# Number Of Atoms
7
# Number Of Groups
1
# Alkane-group
flexible
# number of atoms
7
# atomic positions
0 CH3_sp3
1 CH2_sp3
2 CH2_sp3
3 CH2_sp3
4 CH2_sp3
5 CH2_sp3
6 CH3_sp3
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 6 0 5 0 0 4 0 0 0 0 0 0 6 0
# Bond stretch: atom n1-n2, type, parameters
0 1 HARMONIC_BOND 96500 1.54
1 2 HARMONIC_BOND 96500 1.54
2 3 HARMONIC_BOND 96500 1.54
3 4 HARMONIC_BOND 96500 1.54
4 5 HARMONIC_BOND 96500 1.54
5 6 HARMONIC_BOND 96500 1.54
# Bond bending: atom n1-n2-n3, type, parameters
0 1 2 HARMONIC_BEND 62500 114
1 2 3 HARMONIC_BEND 62500 114
2 3 4 HARMONIC_BEND 62500 114
3 4 5 HARMONIC_BEND 62500 114
4 5 6 HARMONIC_BEND 62500 114
# Torsion n1-n2-n3-n4 type
0 1 2 3 TRAPPE_DIHEDRAL 0.0 335.03 -68.19 791.32
1 2 3 4 TRAPPE_DIHEDRAL 0.0 335.03 -68.19 791.32
2 3 4 5 TRAPPE_DIHEDRAL 0.0 335.03 -68.19 791.32
3 4 5 6 TRAPPE_DIHEDRAL 0.0 335.03 -68.19 791.32
# Intra VDW: atom n1-n2
0 4
0 5
0 6
1 5
1 6
2 6
# Number of config moves
6
# nr fixed, list
5 0 1 2 3 4
5 6 5 4 3 2
4 0 1 2 3
4 6 5 4 3
3 0 1 2
3 6 5 4
1. could you please tell me how to get the parameters of bond stretch, bond bending and especially the parameter of torsion. I think it may have a strong relation with the flexibility of this molecule.
and 2. could you please tell me how you get the critical constant of some rare substance, like ibuprofen, through experiment or some other ways?
I am looking forward your letter, thank you very much!
Critical constants can be taken from handbooks or using google.
The parameters for potentials are taken from force fields that are also published. The functional forms that can be used are described in the manual.