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General / net charge in diffusion
« Last post by sara abbasi on May 09, 2022, 05:47:34 AM »
Dear Prof.Dubbeldum
I had calculate adsorption for a binary mixture using GCMC and there was no warning about net charge. After that I calculated self diffusivity for this mixture by the same input files and using following code. But in my output folder there was net charge warning (the net charge is not zero). What is the reason?  I will be happy if you guide me.

SimulationType                   MolecularDynamics
NumberOfCycles                   10000000
NumberOfInitializationCycles     10000
NumberOfEquilibrationCycles      10000
PrintEvery                       5000
RestartFile                      NO

ContinueAfterCrash               yes
WriteBinaryRestartFileEvery      500

Ensemble                         NVT

UseChargesFromCIFFile            yes
CutOff                           12.0
TimeStep                         0.0005          # (ps)
Forcefield                       Local
EwaldPrecision                   1e-6

Framework 0
FrameworkName Framework_0_final_1_1_1
UnitCells 3 3 1
ExternalTemperature 300.0

ComputeMSD                 yes
WriteMSDEvery              1000
SampleMSDEvery             1000
ComputeIndividualMSD       yes
NumberOfBlockElementsMSD   100

ComputeEnergyHistogram     yes
EnergyHistogramEvery       1000
EnergyHistogramSize        1000

Movies yes
WriteMoviesEvery  1000       

Component 0 MoleculeName               propane
            StartingBead               0
            MoleculeDefinition         local
            MolFraction                0.1
            IdealGasRosenbluthWeight   1.0
            TranslationProbability     1.0
            RotationProbability        1.0
            RegrowProbability          1.0
            CreateNumberOfMolecules    21

Component 1 MoleculeName               propene
            StartingBead               0
            MoleculeDefinition         local
            MolFraction                0.9
            IdealGasRosenbluthWeight   1.0
            TranslationProbability     1.0
            RotationProbability        1.0
            RegrowProbability          1.0
            CreateNumberOfMolecules    104                 

I looked at the potential energy formula in the RASPA manual and found that I need to modify the FEYNMAN_HIBBS_LENNARD_JONES formula into a higher order form to better use it for the correction inside the molecule, but I can't find the place to define this formula expression in the RASPA source package, can you provide me some guidance?
Input files and parameters / Re: two different temperatures
« Last post by SierraEcho on April 22, 2022, 02:11:22 PM »
If you are using MC, the temperature is used to calculate the acceptance ratio. For example, the concept of temperature/velocity can not be extracted from MC as the trajectories don't follow physical laws (actually, there is no physical meaningful trajectory at all).

If your fluid-wall interaction is not temperature dependent an the adsorbent itself is rigid, changing the temperature of the adsorbent shouldn't even make a different for the result of your adsorbate.

Open for a fruitful discussion about that :)

Input files and parameters / two different temperatures
« Last post by Nourissa on April 22, 2022, 10:47:54 AM »
can we create two temperatures one for the adsorbent and another different temperature for the adsorbate?
Input files and parameters / TIP4P model
« Last post by Nourissa on April 21, 2022, 01:20:10 PM »
can anyone share TIP4P model info such as .def file and lennord Jones parameters I want to re check my work couldn't find anything online
Output files / output - molcules/unit cell - IMPORTANT
« Last post by Nourissa on April 21, 2022, 12:03:20 PM »
in the output folder the parameter Molecules per unit cell, does it mean the unit cell we assigned in the beginning of simulation ex( 4 2 2 ) or the simplest unit cell which is (1 1 1).

I want to know if I need to do further calculation to match the exp or this is the final value
My idea was to imitate the steel potential inside a cylindrical pore, however I agree that not so many layers are necessary.

With regard to computational effort, of course it would be way more elegant to define a fluid-wall forcefield like steel potential directly instead of calculating it through the backdoor by summing up
two-body interactions between an adsorbant molecule and the wall.  Nethertheless, directly using steel potential for slit, cylinder and sphere is not possible in raspa, right? Otherwise, I would highly appreciate any hints how I could make my simulation more elegant :)

Regarding "RestrictMovesToCylinder", this sounds reasonable to reduce CPU times. I couldn't find an example, neither in the manual nor in the internet. Therefore, I had a look at the plain C-Code.
For the sake of completeness:

fprintf(FilePtr,"\t\tcylinder center :                   %lf,%lf,%lf\n",Components.RestrictCylinderCenter[j].x,Components.RestrictCylinderCenter[j].y,Components.RestrictCylinderCenter[j].z);
              fprintf(FilePtr,"\t\tcylinder direction :                %s\n",Components.RestrictCylinderDirection[j]==X_DIR?"X":(Components.RestrictCylinderDirection[j]==Y_DIR?"Y":"Z"));
              fprintf(FilePtr,"\t\tcylinder radius :                   %lf\n",Components.RestrictCylinderRadius[j]);

I can't really figure out how to define a cylinder, I guess it should look somehow like:

RestrictMovesToCylinder yes
cylinder x y z x_dir y_dir radius

Your help with the cylinder definition would be highly appreciated! :)

Output files / Re: Energy landscape
« Last post by David Dubbeldam on April 18, 2022, 07:56:22 PM »
Recently, these capabilities are implemented in iRASPA, where you play around with these energy-surfaces on the fly (computed very fast on the GPU).
Many of the moves use biasing (Multiple-first beads method). As soon as overlap is detected the move will be rejected.

Do you really need all the atoms outside the first cylindrical ring? If not, then you could
RestrictMovesToCylinder yes
and define a cylinder. Everything outside the cylinder will be considered an overlap.
General / Re: CIF file
« Last post by David Dubbeldam on April 18, 2022, 07:43:09 PM »
CIF files are published by experimental groups to convert the structural data in a standardized way. The are uploaded to databases like CSD database.
For simulation codes, the atomic information is necessary _input_ for the simulations, because the positions of all the atoms need to be specified.
Programs like 'Openbabel' can convert between many formats.
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