Author Topic: different adsorption isotherms compare to literature  (Read 94 times)

Mozhdeh

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different adsorption isotherms compare to literature
« on: July 17, 2019, 07:56:19 AM »
Dear all
I did some MC simulation to reproduce water adsorption isotherms on MOF-801 but results are not consistent at all. in the literature, water uptake at p/p0=0.2 is about 200 cm3/gr while mine is 0.5 cm3/gr. Molecule and force field definition is the same as literature. Partial charges were found beforehand using Qeq module and finalP1.cif file were used as the input cif. I also changed void fraction up to 0.9 but the impact is not so much! what did I miss? I appreciate any comment.
Regards

P. S. simulation file is as below:

SimulationType                MonteCarlo
NumberOfCycles                50000
NumberOfInitializationCycles  10000
PrintEvery                    10000
RestartFile                   no

chargemethod            Ewald
Forcefield                    GenericMOFs
UseChargesFromCIFFile         yes
cutoffvdw                     12.0
SymmetrizeFrameworkCharges    yes

Framework 0
FrameworkName mof-801-p1
UnitCells 2 2 2
HeliumVoidFraction 0.49
ExternalTemperature 298
ExternalPressure 3456

Component 0 MoleculeName             water
            MoleculeDefinition       TraPPE
            randomTranslationProbability   0.5
            RotationProbability      0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0



David Dubbeldam

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Re: different adsorption isotherms compare to literature
« Reply #1 on: July 17, 2019, 07:57:43 PM »
Are you comparing your simulation to other simulations or your simulations to experiments?
For the latter you need a bigger picture view and compare the simulated isotherm to the experimental one. Usually at some pressure the isotherm shoots up due to water-water clustering, but the details of where that happens depends on many factors (especially defects).
Also, the water-model is never perfect, nor is the force field in general.

Mozhdeh

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Re: different adsorption isotherms compare to literature
« Reply #2 on: July 20, 2019, 12:55:19 PM »
Dear Dr. Dubbeldam
Thanks for the kind response. Actually I compare it with both simulated and experimental results which are consistent in previous literature. I compare my output with the examples of RASPA2 and I noticed that there were no more than 2 number of adsorbent in each cycle, while for example in the Adsorption_of_CO2_in_Flexible_IRMOF-1_Fixed_Volume, number of adsorbents in the last cycle is 39 and the excess loading is 140.3574056061 (avg. 158.7275906778) [cm^3 STP/g]. So I think there is something inhibiting a proper MC simulation. Moreover, I used psuedo_atom.def file to neutralized the charge of water molecules, however the MOF itself has a net charge. So I used randomTranslationProbability   0.5 and ReinsertionProbability   0.0 , but in the MC moves, charges were created on the water molecules (Net charge: 0.964176 (F: 0.000176, A: 0.964, C: 0)).

Here is the properties calculated at the last cycle of my simulation:

[Init] Current cycle: 900000 out of 1000000
========================================================================================================

Net charge: 0.964176 (F: 0.000176, A: 0.964, C: 0)
Current Box:  35.66960   0.00000   0.00000 [A]
               0.00000  35.66960   0.00000 [A]
               0.00000   0.00000  35.66960 [A]
Box-lengths:  35.66960  35.66960  35.66960 Box-angles:   90.00000  90.00000  90.00000 [degrees]
Volume: 45383.15846 [A^3]

Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (water), current number of integer/fractional/reaction molecules: 2/0/0, density:   1.31729 [kg/m^3]
   absolute adsorption:   0.25000 [mol/uc],         0.0420 [mol/kg],              0.7563 [mg/g]
                                                    0.9417 [cm^3 STP/g],          1.6402 [cm^3 STP/cm^3]
   excess adsorption:     0.25000 [mol/uc],         0.0420 [mol/kg],              0.7563 [mg/g]
                                                    0.9417 [cm^3 STP/g],          1.6402 [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 12 0 12 0
Number of Framework-atoms:   2624
Number of Adsorbates:           2 (2 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, 0 reaction

Current total potential energy:            -12224.3694682955 [K]
   Current Host-Host energy:                     0.0000000000 [K]
   Current Host-Adsorbate energy:           -14790.5805795910 [K]
   Current Host-Cation energy:                   0.0000000000 [K]
   Current Adsorbate-Adsorbate energy:        2566.2111112939 [K]
   Current Cation-Cation energy:                 0.0000000000 [K]
   Current Adsorbate-Cation energy:              0.0000000000 [K]

WARNING: THE SYSTEM HAS A NET CHARGE



Mozhdeh

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Re: different adsorption isotherms compare to literature
« Reply #3 on: July 21, 2019, 06:04:36 AM »
Dear all
I test the same MOF adsorption isotherm of N2 at 77 K which behaved normal


Current cycle: 40000 out of 50000
========================================================================================================

Net charge: 0.000176 (F: 0.000176, A: 0, C: 0)
Current Box:  35.66960   0.00000   0.00000 [A]   Average Box:  35.66960   0.00000   0.00000 [A]
               0.00000  35.66960   0.00000 [A]                  0.00000  35.66960   0.00000 [A]
               0.00000   0.00000  35.66960 [A]                  0.00000   0.00000  35.66960 [A]
Box-lengths:   35.66960  35.66960  35.66960 [A] Average:  35.66960  35.66960  35.66960 [A]
Box-angles:   90.00000  90.00000  90.00000 [degrees] Average:  90.00000  90.00000  90.00000 [degrees]
Volume: 45383.15846 [A^3] Average Volume: 45383.15846 [A^3]

Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (N2), current number of integer/fractional/reaction molecules: 302/0/0 (avg. 298.25187), density: 309.54848 (avg. 305.70667) [kg/m^3]
   absolute adsorption:  37.75000 (avg.  37.28148) [mol/uc],   6.3438084017 (avg.   6.2650752004) [mol/kg], 177.7121497852 (avg. 175.5065588236) [mg/g]
                        142.1899676634 (avg. 140.4252435976) [cm^3 STP/g],  247.6738366201 (avg. 244.5999490094) [cm^3 STP/cm^3]
   excess adsorption:    37.7474627383 (avg.  37.1564835879) [mol/uc],   6.3433820202 (avg.   6.2440692123) [mol/kg], 177.7002053553 (avg. 174.9181079965) [mg/g]
                        142.1804107585 (avg. 139.9544158901) [cm^3 STP/g],  247.6571899091 (avg. 243.7798369677) [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 1510 0 1510 0
Number of Framework-atoms:   2624
Number of Adsorbates:         302  (302 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, 0 reaction)

Current total potential energy:           -541892.7820463965 [K]  (avg.     -530686.6081954332)
   Current Host-Host energy:                     0.0000000000 [K]  (avg.           0.0000000000)
   Current Host-Adsorbate energy:          -484779.4158412396 [K]  (avg.     -476688.6897432785)
   Current Host-Cation energy:                   0.0000000000 [K]  (avg.           0.0000000000)
   Current Adsorbate-Adsorbate energy:      -57113.3662051579 [K]  (avg.      -53997.9184521721)
   Current Cation-Cation energy:                 0.0000000000 [K]  (avg.           0.0000000000)
   Current Adsorbate-Cation energy:              0.0000000000 [K]  (avg.           0.0000000000)

WARNING: THE SYSTEM HAS A NET CHARGE


So I think something wrong about the water, maybe the increased charge of it in the MC simulation. Any comment?
Best regards

David Dubbeldam

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Re: different adsorption isotherms compare to literature
« Reply #4 on: July 24, 2019, 01:14:18 PM »
What do you mean with "there were no more than 2 number of adsorbent in each cycle", do you have multiple frameworks? do you mean "adsorbent" which is the framework, or "adsorbate" which means the molecules inside the framework.
"So I think something wrong about the water, maybe the increased charge of it in the MC simulation.", have you tried making it charge-neutral?