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Messages - Kajum Safiullin

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1
General / Re: Issue with ExtraFrameworkMolecule
« on: December 25, 2020, 11:41:41 AM »
Thank you for the reply, I'll try to recompile it.

2
General / Issue with ExtraFrameworkMolecule
« on: December 17, 2020, 11:57:01 AM »
Hello Prof.Dubbeldam,

I am trying to make adsorption MC simulations in LTA structures but always get this error:
Code: [Select]
...
End reading cif-file
Shift all potentials
comp: 0 total: 96
Illegal instruction (core dumped)

It happens to the example code from the Tutorial as well and I found it is connected with this code line:  ExtraFrameworkMolecule         yes  (it works with No)
Code: [Select]
SimulationType                   MonteCarlo
NumberOfCycles                   25000
NumberOfInitializationCycles     10000
RestartFile                      no
PrintEvery                       1000

Forcefield                       GarciaPerez2006
ModifyOxgensConnectedToAluminium yes

Framework 0
FrameworkName LTA4A
RemoveAtomNumberCodeFromLabel yes
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 10000.0

Component 0 MoleculeName                   sodium
            MoleculeDefinition             TraPPE
            TranslationProbability         1.0
            RandomTranslationProbability   1.0
            ExtraFrameworkMolecule         yes
            CreateNumberOfMolecules        96

Component 1 MoleculeName                   CO2
            MoleculeDefinition             TraPPE
            BlockPockets                   yes
            BlockPocketsFilename           LTA
            TranslationProbability         1.0
            ReinsertionProbability         1.0
            SwapProbability                1.0
            ExtraFrameworkMolecule         no
            CreateNumberOfMolecules        0

Any ideas how to solve this issue? RASPA generally worked well for me simulating other structures when this code line is not used.

regards,
Kajum

3
Input files and parameters / Re: Charge equilibration for MOFs
« on: October 18, 2019, 12:15:12 PM »
I would suggest first to check the cif and the header of the output file (framework atoms lines) of the simulation if they state the same number of atoms in your cell. Once I used a quite large cell and amount of atoms was surprisingly reduced if compared with the input structure file.

4
Input files and parameters / Re: Blocking pockets in MD?
« on: October 17, 2019, 11:38:26 AM »
Thank you for the information.
I am using raspa for a somewhat different than a gas in zeolite-like structures with closed pores, the system and its conditions are different to ones usually used in raspa simulations. However I found raspa as a nice code that suits my basic requirements for simple initial tests of a complicated system after some modifications of my structure with a side-pocket (as you called it). I'll think on new mods to solve my problem with MD.

5
Input files and parameters / Blocking pockets in MD?
« on: October 16, 2019, 04:42:04 PM »
Hi everyone,

I have to use blocking pockets in both MC and MD simulations. It works fine with MC, but doesn't work during MD simulations at all: gas molecules keep going inside the blocked pockets (they have open geometry in my case and are not surrounded by framework atoms). Any ideas how to solve this issue?

I will appreciate any help.

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