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Dear Professor,

Thanks for the swift reply. As I have mentioned earlier, the simulation box size (number of unit cells in x y z directions), cutoff-distance, tail corrections, force fields, etc., all were the same. The framework structure was also taken from the same reference.  The only difference I could find is the type of ensemble (Gibbs ensemble vs GCMC). Could this be the reason? Can this have a difference of 0.5mol/Kg?

Thanks and regards

Respected Prof. Dubbeldam

I am trying to replicate the adsorption isotherm on a zeolite, from the literature. In the literature, they have used Gibbs ensemble to study the adsorption on a zeolite. Using GCMC in RASPA, I tried to replicate the same thing. However, I am getting lower values compared to the literature. A constant difference of 0.5 mmol/g is being obtained at all pressures (0.1 bar to 10 bar). All the force fields, molecule models, and structure are the same. Could the difference in the ensemble, (or difference in the code) be the reason for this difference of 0.5 mmol/g?

Thanks and regards

Thank you for the reply professor.

"For atom-types that have no VDW interaction, the atoms can be placed on top of other atoms during the test. This lead to large errors in the energy/force interpolation, but this would not occur during a real simulation."  Could you please elaborate on this point??

I am not able to understand, why the lone pair pseudo atom alone is showing error while using grid energy interpolation.

Also, for example, let us say I have made a grid for H, S, and L (of H2S), and C and O (of CO2). Now, in the final simulation, I call only H, S, C, and O grids alone, for interpolation. Is this approach appropriate? Can I expect that the energies (VDW and coloumbic) of 'L' with the framework are calculated separately?

Awaiting for your reply.

Thank you.

[1.]

Dear Professor,

1. I am doing gas adsorption studies using GCMC.  To speed up my simulations, I have used the Grid option. By using the following input file, I am able to make energy grid.

Input file_1
SimulationType  MakeGrid

Forcefield      test
UseChargesFromCIFFile   yes

CutOff                        14.0

ChargeMethod                  Ewald
EwaldPrecision                1e-10

Framework 0
FrameworkName  framework
UnitCells 2 2 5
ExternalTemperature 298.0

NumberOfGrids 3
GridTypes H_s S_s S_com
SpacingVDWGrid 0.1
SpacingCoulombGrid 0.1
Input file end

I have used H2S molecule (4-3 Trappe model). There is one lone pair which is defined as an atom. So, in the .def file I have included "0 3 RIGID_BOND" command, to define the third bond. I have given S_com  notation for it.
Now, I used these grids for adsorption studies (GCMC), to speed the simulations. But I am getting a warning something like "Energy density interpolation probably not accurate enough". As I checked, Boltzmann relative error was very high for S_com only.  Other atoms doesn't have any error. The input file is as follows.

Input file_2
SimulationType                MonteCarlo
NumberOfCycles                50000
NumberOfInitializationCycles  50000
PrintEvery                    1000

Forcefield                    test
UseChargesFromCIFFile         yes

CutOff                        14.0

ChargeMethod                  Ewald
EwaldPrecision                1e-6

Framework 0
FrameworkName framework
UnitCells 2 2 5
ExternalTemperature 298.0
ExternalPressure 1e5

NumberOfGrids 3
GridTypes H_s S_s S_com
SpacingVDWGrid 0.1
SpacingCoulombGrid 0.1
UseTabularGrid yes

Component 0 MoleculeName                     H2S
            MoleculeDefinition               TraPPE
            TranslationProbability           0.5
            RotationProbability              0.5
            SwapProbability                  1.0
            CreateNumberOfMolecules          0
Input file end

I have used the correct grid, and the parameters are also the same. Can you suggest a way to overcome this error?


Thank you.

Thank you very much for the reply, Professor.

I was running the simulations at 11 different pressures (0.1,0.3,0.5,0.7,0.9,1,2,4,6,8,10). The simulations at low pressure (below 1bar) are starting after a gap of around 5-8 hours. But the ones at high pressures are not even starting. When I do any changes in the input file (I have changed the 'WriteBinaryRestartFileEvery' to 5000 from 10000), before re-starting them using the binary file, then it starts fresh from zero (as can be seen in the output file).
I configured RASPA using gcc compiler in the first cluster. Later, I moved the data to another cluster to run the simulations there. In the new cluster, RASPA was configured using gcc compiler, but a different version. I am guessing this might be the reason.
Also, is there anything I can do while configuring RASPA, so that it speeds the simulations?

Thank you again.

Thank you very much for the reply.

1. I have installed RASPA 2.0 in both the clusters (gcc compiler). My earlier calculations were done using RASPA 2.0, so I am continuing with that.

2. Sorry, by "CrashRestart  yes", I meant the 'Binary Restart File'. In the input file, I have added "ContinueAfterCrash   yes" command, to continue using the binary file in the folder "Crash Restart".

3. I have tried the two options given in the manual as follows, (following are the input file commands I have given for a GCMC simulation, with 200000 initialization and production cycles, each)
Approach 1: (using restart file, where the positions are taken)

SimulationType            MonteCarlo
NumberOfCycles                188800
PrintEvery                    200

PrintPropertiesEvery          200

RestartFile                   yes
WriteBinaryRestartFileEvery   10000

Approach 2: (using binary restart file (crash restart))
SimulationType            MonteCarlo
NumberOfCycles                200000
NumberOfInitializationCycles  200000
PrintEvery                    200

PrintPropertiesEvery          200

ContinueAfterCrash            yes
WriteBinaryRestartFileEvery   10000



So, in the first approach I have to change, in the input file, the number of production and initialization cycles accordingly. But, the problem here is, the earlier averages of the properties are ignored and being calculated from the current value.

The second approach, where I include a command in the input file ("ContinueAfterCrash   yes"), is working properly. It is exactly picking up from where it has left without changing anything else in the input file. But, when I start the simulations using this command, it is taking a long time to restart. Every time my wall time is reached, they stop and take a long time to pick up from where it has left.
Is there anything I can do to overcome this and speed up the calculations?


Thank you,

Best regards,
Suvardhan J.

Dear Professor,

I am using RASPA to study the adsorption of a gas on a MOF. I have transferred my jobs from one cluster to another cluster, (after killing the jobs). In the new cluster, I have submitted the jobs, using 'CrashRestart    yes' command. I haven't changed anything else in the input file. I have 11 different files (each for a particular pressure). The simulations are taking almost 24 hours to pick up from where they have left. Also, the ones with high pressure (above 1 bar) are not running (I presume that it is still reading the Crash restart file). Is there a way I can speed up my calculations during using the 'Crash Restart'?

Thanks,

Regards,
Vardhan.