Author Topic: Excess adsorption  (Read 312 times)

Junran Lu

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Excess adsorption
« on: July 26, 2018, 02:31:59 AM »
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

David Dubbeldam

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Re: Excess adsorption
« Reply #1 on: July 27, 2018, 08:12:40 PM »
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).

Junran Lu

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Re: Excess adsorption
« Reply #2 on: July 28, 2018, 03:00:03 AM »
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!

David Dubbeldam

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Re: Excess adsorption
« Reply #3 on: July 29, 2018, 11:52:41 AM »
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).