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Topics - Kajum Safiullin

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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.


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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