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#11
General / How to change the atom index i...
Last post by kokojiang - October 24, 2023, 06:56:23 AMDear all,
I have the cif file of the MOF structure, the atoms and their indexes goes like this:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C3 1.0 0.9812 0.86236 0.85294
C4 1.0 0.29174 0.5265 0.71863
...
C1185 1.0 0.17108 0.59341 0.61745
C1186 1.0 0.14289 0.58226 0.66194
C1187 1.0 0.1861 0.67126 0.70408
Cr1188 1.0 0.25915 0.66547 0.69122
...
But in the simulation, we divided the atoms to different types,e.g. only 3 types of carbon atom and 2 types of Cr and so on. The force field is made for the type of atoms such as:
C1 lennard-jones 47.8562 3.47299
C2 lennard-jones 47.8562 3.47299
Cr1 lennard-jones 7.54829 2.69319
Cr2 lennard-jones 7.54829 2.69319
So the data need to be like:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C1 1.0 0.9812 0.86236 0.85294
C2 1.0 0.29174 0.5265 0.71863
...
C1 1.0 0.17108 0.59341 0.61745
C1 1.0 0.14289 0.58226 0.66194
C2 1.0 0.1861 0.67126 0.70408
Cr2 1.0 0.25915 0.66547 0.69122
...
How do I change the atom index? There are too many atoms for me to do it manually. Is there any software that can do this ?
I have the cif file of the MOF structure, the atoms and their indexes goes like this:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C3 1.0 0.9812 0.86236 0.85294
C4 1.0 0.29174 0.5265 0.71863
...
C1185 1.0 0.17108 0.59341 0.61745
C1186 1.0 0.14289 0.58226 0.66194
C1187 1.0 0.1861 0.67126 0.70408
Cr1188 1.0 0.25915 0.66547 0.69122
...
But in the simulation, we divided the atoms to different types,e.g. only 3 types of carbon atom and 2 types of Cr and so on. The force field is made for the type of atoms such as:
C1 lennard-jones 47.8562 3.47299
C2 lennard-jones 47.8562 3.47299
Cr1 lennard-jones 7.54829 2.69319
Cr2 lennard-jones 7.54829 2.69319
So the data need to be like:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C1 1.0 0.9812 0.86236 0.85294
C2 1.0 0.29174 0.5265 0.71863
...
C1 1.0 0.17108 0.59341 0.61745
C1 1.0 0.14289 0.58226 0.66194
C2 1.0 0.1861 0.67126 0.70408
Cr2 1.0 0.25915 0.66547 0.69122
...
How do I change the atom index? There are too many atoms for me to do it manually. Is there any software that can do this ?
#12
Visualization / Re: Density Plot
Last post by Lingxiao Qin - September 29, 2023, 03:06:14 PMAre you sure your DensityProfile.vtk file is correct? It seems the file should contain totally 3375000 data points, but you just list 10 points. (Maybe you omit other data points for clarity?) Check /RASPA/RASPA2/examples/Visualization/FullCell/Density/MFI/hexane/RASPA/simulation.input for a sample input file. By the way, iRASPA can import the DensityProfile.vtk file generated by RASPA (with a newest version) to visualize the density plot, but I find it lacks some functions such as displaying the colorbar. Perhaps you can try iRASPA to see if it can generate the correct results.
#13
General / Inquiry regarding RASPA calcul...
Last post by Temoor - September 28, 2023, 06:26:45 PMHi all,
I have a 3 questions to discuss regarding GCMC by RASPA.
1) I believe that the default calculation of adsorption in RASPA is through GCMC. Is it correct?
2) If yes (refer to question 1), how does the RASPA calculating the chemical potential during the adsorption calculation (as I am not inputting any chemical potential in the input file) and I cannot see the chemical potential printed in the output file. For example, please see this tutorial example from RASPA github: https://github.com/iRASPA/RASPA2/tree/master/examples/Basic/7_Adsorption_of_Methane_in_MFI/Output/System_0
3) The GCMC is calculating the total number of molecules in porous system. If the pores are small let's say 1A, we could say that the number of molecules is equal to the adsorbed phase in that confined pore. However, if the pores are larger (let's say 3nm ~ 30A), there is a significant free gas in the system in the middle region and I believe that the total number of molecules will not correspond to the adsorbed molecules. However, RASPA is considering number of molecules = adsorbed molecules in the calculation and provide final results based on this assumption. Do you think I need to subtract the free gas molecules from the calculation to get an actual adsorption value.
I believe these are some basic questions, but I need the clarity for generating accurate results.
Thanks,
Temoor
I have a 3 questions to discuss regarding GCMC by RASPA.
1) I believe that the default calculation of adsorption in RASPA is through GCMC. Is it correct?
2) If yes (refer to question 1), how does the RASPA calculating the chemical potential during the adsorption calculation (as I am not inputting any chemical potential in the input file) and I cannot see the chemical potential printed in the output file. For example, please see this tutorial example from RASPA github: https://github.com/iRASPA/RASPA2/tree/master/examples/Basic/7_Adsorption_of_Methane_in_MFI/Output/System_0
3) The GCMC is calculating the total number of molecules in porous system. If the pores are small let's say 1A, we could say that the number of molecules is equal to the adsorbed phase in that confined pore. However, if the pores are larger (let's say 3nm ~ 30A), there is a significant free gas in the system in the middle region and I believe that the total number of molecules will not correspond to the adsorbed molecules. However, RASPA is considering number of molecules = adsorbed molecules in the calculation and provide final results based on this assumption. Do you think I need to subtract the free gas molecules from the calculation to get an actual adsorption value.
I believe these are some basic questions, but I need the clarity for generating accurate results.
Thanks,
Temoor
#14
Input files and parameters / Crash restart
Last post by mhaeri - September 16, 2023, 03:50:30 AMHi,
I am running an isotherm set point on cluster and therefore need to restart it every few days.
recently the simulations have been crashing with Out Of Memory error.
I am trying to start with a higher memory request but it won't restart or start from scratch.
Right now I am getting the following error:
read binary file
DONE!!!
Error in binary restart-file (ReadRestartFramework)
read binary file
DONE!!!
Error in binary restart-file (ReadRestartFramework)
Input error in 'Component'-command: the number of the component 0 is already taken
where lies the problem?
Thanks
Mas Haer
I am running an isotherm set point on cluster and therefore need to restart it every few days.
recently the simulations have been crashing with Out Of Memory error.
I am trying to start with a higher memory request but it won't restart or start from scratch.
Right now I am getting the following error:
read binary file
DONE!!!
Error in binary restart-file (ReadRestartFramework)
read binary file
DONE!!!
Error in binary restart-file (ReadRestartFramework)
Input error in 'Component'-command: the number of the component 0 is already taken
where lies the problem?
Thanks
Mas Haer
#15
General / Quantitative density profile i...
Last post by Temoor - September 14, 2023, 07:34:10 PMHi,
I wanted to create a density profile while running my GCMC. My system has two slabs separated by vacant pore and I wanted to see the fluid density in the middle pore. A picture of how exactly I wanted the profile is attached. Can you please help me with that.
Thanks
I wanted to create a density profile while running my GCMC. My system has two slabs separated by vacant pore and I wanted to see the fluid density in the middle pore. A picture of how exactly I wanted the profile is attached. Can you please help me with that.
Thanks
#16
Output files / Re: Enthalpy of adsorption "na...
Last post by chenyaxin - August 31, 2023, 09:34:41 AMI also encountered the same problem in the process of carbon dioxide adsorption by LTA4A molecular sieve containing Na ions. I checked the force field file and input file which taken from raspa's user manual ,but I did not solve the problem. So I would like to ask you how to solve it. I would appreciate it very much if you could reply to my questions.
#17
Input files and parameters / No VDW interaction
Last post by CharleneZ - August 29, 2023, 09:53:57 PMI am getting an error regarding no VDW interaction for some molecules. I have defined the appropriate molecules to the force_field_mixing_rules to the file, but I still get the error. Is there anything immediately wrong with the file below? I am not sure how to erase this issue. When running the simulation I get the error below:
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION CH4-C1 CH4-C2 CH4-C3 CH4-C4 C1-CH4 C1-C2 C1-C3 C1-C4 C2-CH4 C2-C1 C2-C3 C2-C4 C3-CH4 C3-C1 C3-C2 C3-C4 C4-CH4 C4-C1 C4-C2 C4-C3 (maximum 50 interactions shown)
My force_field_mixing_rules.def file is below:
# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
9
# type interaction, parameters. IMPORTANT: define shortest matches first, so that more specific ones overwrites these
C1 lennard-jones 47.0 3.74
C2 lennard-jones 47.86 3.47
C3 lennard-jones 47.86 3.47
C4 lennard-jones 47.86 3.47
CH4 lennard-jones 158.5 3.72
CH3 lennard-jones 108.0 3.76
CH2 lennard-jones 56.0 3.96
CH lennard-jones 17.0 4.67
C lennard-jones 0.8 6.38
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
Any help is appreciated!
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION CH4-C1 CH4-C2 CH4-C3 CH4-C4 C1-CH4 C1-C2 C1-C3 C1-C4 C2-CH4 C2-C1 C2-C3 C2-C4 C3-CH4 C3-C1 C3-C2 C3-C4 C4-CH4 C4-C1 C4-C2 C4-C3 (maximum 50 interactions shown)
My force_field_mixing_rules.def file is below:
# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
9
# type interaction, parameters. IMPORTANT: define shortest matches first, so that more specific ones overwrites these
C1 lennard-jones 47.0 3.74
C2 lennard-jones 47.86 3.47
C3 lennard-jones 47.86 3.47
C4 lennard-jones 47.86 3.47
CH4 lennard-jones 158.5 3.72
CH3 lennard-jones 108.0 3.76
CH2 lennard-jones 56.0 3.96
CH lennard-jones 17.0 4.67
C lennard-jones 0.8 6.38
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
Any help is appreciated!
#18
Output files / Re: Enthalpy of adsorption "na...
Last post by dddD - August 27, 2023, 02:41:40 PMi meet the same question. I want to know how to calculate enthalpy of adsorption in this simulation.
#19
Visualization / Density Plot
Last post by saif - August 21, 2023, 06:49:01 PMHi,
I'm seeking advice.
I'm attempting to plot the DensityProfile.vtk file that I obtained from my simulation run. However, I'm encountering an issue where the plot appears completely white without any visible content.
All the data inside the file consists of very small values.
-----------------------------------------------------------
Part of my file:
# vtk DataFile Version 1.0
CELL_PARAMETERS 19.152000 19.152000 19.152000 90.000000 90.000000 90.000000
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 150 150 150
ORIGIN 0.000000 0.000000 0.000000
SPACING 0.127680 0.127680 0.127680
POINT_DATA 3375000
SCALARS scalars double
LOOKUP_TABLE default
0
0.000584217
0.00084387
0.00183199
0.00266144
0.00421935
0.00569792
0.00809249
0.00786169
0.0121387
-----------------------------------------------------------
Thank you
I'm seeking advice.
I'm attempting to plot the DensityProfile.vtk file that I obtained from my simulation run. However, I'm encountering an issue where the plot appears completely white without any visible content.
All the data inside the file consists of very small values.
-----------------------------------------------------------
Part of my file:
# vtk DataFile Version 1.0
CELL_PARAMETERS 19.152000 19.152000 19.152000 90.000000 90.000000 90.000000
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 150 150 150
ORIGIN 0.000000 0.000000 0.000000
SPACING 0.127680 0.127680 0.127680
POINT_DATA 3375000
SCALARS scalars double
LOOKUP_TABLE default
0
0.000584217
0.00084387
0.00183199
0.00266144
0.00421935
0.00569792
0.00809249
0.00786169
0.0121387
-----------------------------------------------------------
Thank you
#20
General / Density Histogram from GCMC si...
Last post by Cigdem - August 16, 2023, 08:32:36 AMDear Prof. Dubbeldam and dear RASPA Community,
With adding these lines to the simulation input, we can obtain density profiles as a result of the GCMC simulation:
ComputeDensityProfile3DVTKGrid yes
WriteDensityProfile3DVTKGridEvery 1000
DensityProfile3DVTKGridPoints 150 150 150
AverageDensityOverUnitCellsVTK yes
DensityAveragingTypeVTK FullBox
FreeEnergyAveragingTypeVTK FullCell
However, we encounter a problem when we want to run GCMC simulations to obtain density profiles from four-component gas mixture adsorption in a MOF.
The error message is long but starts and ends as given below:
" *** Error in `simulate': free(): invalid next size (normal): 0x000056087ce427e0 ***
......
....
..
.
/var/spool/slurm/d/job5763373/slurm_script: line 67: 14511 Aborted $COMMAND $INPUT
RASPA finished. Return code is 134".
I tried with different cif files and different gas definitions, but, as far as I note, it only happens when I run the simulation for a mixture of more than three components.
I would be glad to learn if there is something that I am missing and avoids the production of density profiles for a mixture of more than three components.
Thank you,
With adding these lines to the simulation input, we can obtain density profiles as a result of the GCMC simulation:
ComputeDensityProfile3DVTKGrid yes
WriteDensityProfile3DVTKGridEvery 1000
DensityProfile3DVTKGridPoints 150 150 150
AverageDensityOverUnitCellsVTK yes
DensityAveragingTypeVTK FullBox
FreeEnergyAveragingTypeVTK FullCell
However, we encounter a problem when we want to run GCMC simulations to obtain density profiles from four-component gas mixture adsorption in a MOF.
The error message is long but starts and ends as given below:
" *** Error in `simulate': free(): invalid next size (normal): 0x000056087ce427e0 ***
......
....
..
.
/var/spool/slurm/d/job5763373/slurm_script: line 67: 14511 Aborted $COMMAND $INPUT
RASPA finished. Return code is 134".
I tried with different cif files and different gas definitions, but, as far as I note, it only happens when I run the simulation for a mixture of more than three components.
I would be glad to learn if there is something that I am missing and avoids the production of density profiles for a mixture of more than three components.
Thank you,