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Messages - Junran Lu

#1
Output files / absoulte and excess adsorption
May 24, 2024, 04:09:26 AM
Dear  Professor David:
In the simulation of toluene adsorption on MFI-type zeolite,  the output-file shows, adsorption load is postive, and excess load is negative; in the simluation.input, we set the external temperature and pressure are 298K and 1e5Pa, respeactively;  which adsorption result is correct under 298K/1e5Pa tolulene adsorption simulation?

the detail amount of adsorption is following:

Component 0 [toluene]
-------------------------------------------------------------
    Block[ 0] 57.54390           [-]
    Block[ 1] 61.49325           [-]
    Block[ 2] 62.96655           [-]
    Block[ 3] 63.05500           [-]
    Block[ 4] 64.06460           [-]
    ------------------------------------------------------------------------------
    Average                                     61.8246600000 +/-       4.5842966097 [-]
    Average loading absolute [molecules/unit cell]        7.7280825000 +/-       0.5730370762 [-]
    Average loading absolute [mol/kg framework]          1.3397983817 +/-       0.0993460082 [-]
    Average loading absolute [milligram/gram framework]        123.4325701655 +/-       9.1525212259 [-]
    Average loading absolute [cm^3 (STP)/gr framework]         30.0302084340 +/-       2.2267390183 [-]
    Average loading absolute [cm^3 (STP)/cm^3 framework]         54.7548092722 +/-       4.0600673988 [-]

    Block[ 0] 57.54390           [-]
    Block[ 1] 61.49325           [-]
    Block[ 2] 62.96655           [-]
    Block[ 3] 63.05500           [-]
    Block[ 4] 64.06460           [-]
    ------------------------------------------------------------------------------
    Average                                    -24.1753400000 +/-       4.5842966097 [-]
    Average loading excess [molecules/unit cell]       -3.0219175000 +/-       0.5730370762 [-]
    Average loading excess [mol/kg framework]         -0.5239022974 +/-       0.0993460082 [-]
    Average loading excess [milligram/gram framework]        -48.2659241607 +/-       9.1525212259 [-]
    Average loading excess [cm^3 (STP)/gr framework]        -11.7427333877 +/-       2.2267390183 [-]
    Average loading excess [cm^3 (STP)/cm^3 framework]        -21.4108113298 +/-       4.0600673988 [-]


while during the simluation, the toluene molecule is defined as a rigid molecule(as following):
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
591.75
4126257.975
0.264
# Number Of Atoms
7
# Number Of Groups
1
# Alkane-group
7
rigid
0 CH3  0.0       1.54    0.0
1 C_arc    0.0       0.0     0.0
2 CH_arc   1.2124   -0.7     0.0
3 CH_arc   1.2124   -2.1     0.0
4 CH_arc   0.0      -2.8     0.0
5 CH_arc   -1.2124  -2.1     0.0
6 CH_arc  -1.2124   -0.7     0.0
# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
               0    7            0    0            0       0        0            0         0            0         0               0            0        0            0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
3 4 RIGID_BOND
2 3 RIGID_BOND
4 5 RIGID_BOND
5 6 RIGID_BOND
6 1 RIGID_BOND
# Number of config moves
0




#2
Prof. Dubbeldam,

Thank you very much for the answer.  :)
#3
Hi, David Professor:

In the advance examples, Reactive ensemble is introduced in example 6. For each component, the partionfunction was set to different values based on the kind of reactants and products. Is there any principles to set up the partionfunction of reactants and products?

Thanks very much!
Looking forward to your reply!
#4
Output files / Re: Excess adsorption
July 28, 2018, 04:00:03 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!
#5
Output files / Excess adsorption
July 26, 2018, 03:31:59 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
#6
Output files / Re: MSD calculation
May 29, 2018, 11:06:19 AM
Professor David, Thanks very much! I will have a try following your advice!
#7
Output files / Re: MSD calculation
May 02, 2018, 10:46:12 AM
Dear Professor David:

In the resulting file of MSD calculation, the printed time-interval increased with different period in the msd_*.dat file. Such as the first 25 printed time with  internal of 0.0005 Ps, and the next 24 printed time with  internal of 0.0125 Ps, and more, the next following 24 printed time with internal of 0.3125 Ps .......7.8125 Ps,195.312 Ps, and the final 8 printed time with  internal of 4882.81 Ps. And there are any settings to keep the interval as a constant?
Besides, the total printed time (43945.3 Ps) is not equal to the time step (0.0005 Ps) multiplied the NumberOfCycles (100000000). The following is the input file of on the MSD calculation. And more, is there any restrictions on the NumberOfInitializationCylces and NumberOfEquilibrationCycles when setting?

#########################################
Simulationtype                MolecularDynamics
NumberOfCycles              100000000
NumberOfInitializationCylces 500000
NumberOfEquilibrationCycles 10000
PrintEvery                            10000
RestartFile                            No

Ensemble                             NVT
Forcefield                             local
Cutoff                                  12.0
Timestep                              0.0005

Framework                           0
FrameworkName                   ZIF-8
Unitcell                                2 2 4
RemoveAtomNumberCodeFromLabel yes

ExternalTemperature           298.0
ComputeMSD                     yes
PrintMSDEvery                    10000

Component   MoleculeName   N2
                   StarteingBead   0
                   MoleculeDefinition  TraPPE
                   TranslationProbability  1.0
                   RotationProbability  1.0
                   ReinsertionProbability  1.0
                   CreatNumberOfMolecules 5
#########################################

Looking forward to your reply!
Best wishes!
#8
Output files / Question on "Randomlysubstitute"
April 26, 2018, 08:42:51 AM
Hi, Professor David:

In zeolites, the Si atoms were replaced with Al atoms could generate the acidic sites, while the extra-framework-atoms are need to balance charges. However, when I substitute the Si atoms with Al atoms, the resulting structure, namely, Framework_0_final_*_*_*_P1.cif in the directory of Movies/System_0, does not obey the Lowenstein's rule (there exist the Al-O-Al linkage). While The corresponding .data file in the directory of Output/System_0 clearly mark out the "Lowentstein's rule obeyed by framework".
But, I do the calculation again, the resulting structure obey the Lowenstein's rule.

The followings are the simulation.input on the substitution:

SimulationType                            MonteCarlo
NumberOfCycles                          0
Numberofintializtioncycles             0
PrintEvery                                   10
Forcefield                                    GenericZeolites

RandomlySubstitute                    6 Si Al
Framework                                 0
FrameworkName                         EAB
Unitcell                                       3 3 2
ExternalTemperature                   298.0

#The EAB framework was removed the symmetry to P1 and remove all the Si atom were labelled as Si without the index number.
#9
Output files / Re: MSD calculation
April 26, 2018, 08:20:30 AM
Professor David , Thank you very much! :)
#10
Output files / MSD calculation
April 21, 2018, 03:35:08 AM
Hi Professor David:

In the diffusion modeling for single component (such as N2), there are four .dat file generated, namely, msd_self_N2_0.dat, msd_self_total_0.dat, msd_onsager_N2_0_N2_0.dat and msd_onsager_total.dat. And I want to calculate the diffusion coefficient of N2, which one .dat file could be used?
Moreover, for multiple components, if I want calculate the diffusion coefficient for each one, should I use the corresponding msd_self_total_0/1/2.dat ?

Thanks very much!
Best wishes!
#11
Hi, Professor David:

sorry so late to reply you!
Recently, I have been doing the substitution Si atom by Al atom, and more, want to simulate the N2 adsorption in Al-substituted zeolites. And one more question on the extra-framework-molecule definition. In the pseudo_atom.def (Genericzeolites force-filed), I found the Na, Ca and Cl ions are with the same radii, namely, 1.0 A. And if I want use the K atoms as the extra framework molecule, the radii of K atom is set to 1.0 A ? if so,  how to consider the effect of different radii on the adsorption behavior?

Thanks for your reply!
Best Wishes!
#12
Hi, David Professor:

Thanks for your reply. One more question: if I use the "0.0, 0.0, 0.0" to represent the "critical constants" values´╝î is that to say the fugacity is equal to 1?
Thank you very much!

Best wishes!
#13
Hi, David Professor:

In the molecules/TraPPE dictionary, the "critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]" of some molecules were set to "0.0, 0.0, 0.0", such as 3mC9, 4mC9 and BDC. The numbers of "0.0, 0.0, 0.0" means unknown ? Besides, if I don't know of the "critical constants" of a specific molecules, could use the "0.0, 0.0, 0.0" to represent the "critical constants" values?

Thanks very much!
Looking forward to your reply!
Best Wishes!
#14
Input files and parameters / Re: Minimization
April 10, 2018, 04:35:53 AM
Hi, David Professor, I am sorry to reply so late. Thanks for your suggestions.
#15
Input files and parameters / Minimization
April 04, 2018, 11:31:19 AM
Hi, David Professor:
Those structures in RASPA sub-directory, for instance, FAU.cif, MFI_SI.cif, MOR.cif and so on, are minimized by Minimization task? Besides, I found that  in the examples on Minimization task, the options "FlexibleFramework and FrameworkDefinitions" are declared. and those options are mandatory in Minimization task?
Thank you very much!