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Topics - Junran Lu

#1
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!
#2
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
#3
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.
#4
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!
#5
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!
#6
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!
#7
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!
#8
Hi, everyone, when I try to simulation the N2 adsorption in flexible Metal-Organic Frameworks´╝îin the simulation.input file, it is mandatory to use the "FrameworkDefinitions" ? Could I just use the "FlexibleFramework" option to tell the RASAP code the framework is flexible? if the "FrameworkDefinitions" is mandatory, and how could I edit or generate the file?
#9
Input files and parameters / The usage of block_file
March 19, 2018, 06:57:03 AM
Hi, everyone, I have been using the RASPA code to study the N2 adsorption in Zeolites, it is known that some of cages in zeolites need to be blocked, however, if there not exist a corresponding *.block file, can I use the  *.block file as a attachment to the simulation.input to calculate the N2 adsorption? and if ok, what should I do?