Coadsorption in framework
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6 years 1 month ago #478
by M.ERDOS
Dear Cassandra Users,
I am trying to simulate coadsorption of water and trichlorophenol (TCP) in zeolites. I tried to do simulations with interchanging the order of species in the input file. I expected to obtain identical adsorption isotherms but because of some reason I obtain different isotherms with different order of species (1. framework, 2. water, 3. TCP vs 1. framework, 2. TCP, 3. water). I have attached my input files and the resulting isotherms. Did I make any mistake in my input files or is there another problem I am not noticing?
I am looking forward to your comments. Thank you for your help in advance.
Best regards,
Máté
I am trying to simulate coadsorption of water and trichlorophenol (TCP) in zeolites. I tried to do simulations with interchanging the order of species in the input file. I expected to obtain identical adsorption isotherms but because of some reason I obtain different isotherms with different order of species (1. framework, 2. water, 3. TCP vs 1. framework, 2. TCP, 3. water). I have attached my input files and the resulting isotherms. Did I make any mistake in my input files or is there another problem I am not noticing?
I am looking forward to your comments. Thank you for your help in advance.
Best regards,
Máté
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- ryangmullen
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6 years 1 month ago #479
by ryangmullen
Hi Máté,
Have you looked at the fluctuations in the number of molecules in your simulations? In the files you uploaded, the number of TCP molecules are not changing. That suggests your loading results are highly correlated with your initial conditions, not that the ordering of the species is influencing your results.
Ryan
Have you looked at the fluctuations in the number of molecules in your simulations? In the files you uploaded, the number of TCP molecules are not changing. That suggests your loading results are highly correlated with your initial conditions, not that the ordering of the species is influencing your results.
Ryan
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6 years 1 month ago #480
by M.ERDOS
Dear Ryan,
Thank you for your fast reply! I am sorry, my previous post was a bit misleading. The files that I uploaded with the previous post are the results after the restart of the simulations. Please find the original inputs with the starting configurations attached. Both simulations are started with the same initial configuration (empty framework) and you can see that they converge to different TCP adsorption values. I would have expected them to converge to the same regardless of the different seeds (statistically they should, right?) and changing the order. What do you think about this? Is this more system (coadsorption in the framework) related or I am doing something wrong in the inputs?
Thank you for your answer in advance.
Best regards,
Máté
Thank you for your fast reply! I am sorry, my previous post was a bit misleading. The files that I uploaded with the previous post are the results after the restart of the simulations. Please find the original inputs with the starting configurations attached. Both simulations are started with the same initial configuration (empty framework) and you can see that they converge to different TCP adsorption values. I would have expected them to converge to the same regardless of the different seeds (statistically they should, right?) and changing the order. What do you think about this? Is this more system (coadsorption in the framework) related or I am doing something wrong in the inputs?
Thank you for your answer in advance.
Best regards,
Máté
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6 years 1 month ago - 6 years 1 month ago #481
by ryangmullen
Hi Máté,
"am doing something wrong in the inputs?" Your input files look fine.
"I would have expected them to converge to the same regardless of the different seeds (statistically they should, right?)" Yes, equilibrium loading is independent of random number seeds, ordering of species, and initial configuration. However, your initial configuration can effect how long it takes your simulation to reach equilibrium. From your files, it appears that your initial configuration (an empty framework) is quite far from equilibrium. In contrast, you could choose to start from any of the following initial configurations:
Looking at the property files you uploaded, the framework rapidly fills with molecules in the first 10 million MC steps. However, since Cassandra chooses the order of attempted insertions randomly, one of your sims fills first with water molecules, leaving relatively little room for TCP molecules. The other sim fills first with TCP molecules, and as a result has much less room for water. Plotting the number of TCP molecules vs MC step shows the fluctuations in TCP molecules drops drastically after 10-20 million steps. From that point onward, your sampling of the composition of the adsorbed fluid appears to be very slow.
Ryan
"am doing something wrong in the inputs?" Your input files look fine.
"I would have expected them to converge to the same regardless of the different seeds (statistically they should, right?)" Yes, equilibrium loading is independent of random number seeds, ordering of species, and initial configuration. However, your initial configuration can effect how long it takes your simulation to reach equilibrium. From your files, it appears that your initial configuration (an empty framework) is quite far from equilibrium. In contrast, you could choose to start from any of the following initial configurations:
- a framework filled with 1500 water molecules
- a framework filled with 250 TCP molecules
- a framework filled with 1000 water and 100 TCP molecules
Looking at the property files you uploaded, the framework rapidly fills with molecules in the first 10 million MC steps. However, since Cassandra chooses the order of attempted insertions randomly, one of your sims fills first with water molecules, leaving relatively little room for TCP molecules. The other sim fills first with TCP molecules, and as a result has much less room for water. Plotting the number of TCP molecules vs MC step shows the fluctuations in TCP molecules drops drastically after 10-20 million steps. From that point onward, your sampling of the composition of the adsorbed fluid appears to be very slow.
Ryan
Last Edit: 6 years 1 month ago by ryangmullen.
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6 years 1 month ago #483
by M.ERDOS
Dear Ryan,
In the meanwhile I tried to run the simulations with different initial configurations. For example I tried to run simulations with 150 TCP molecules in the framework as initial configuration. I created this starting configuration two ways:
1. by letting Cassandra create the 150 TCPs randomly (make_config)
2. Run a NVT simulation with 500 000 MC steps for 150 randomly created TCPs in the framework
Unfortunately, when I tried to use these initial configurations I got the following error message: "Attempted to delete molecule XXX of species YYY but the molecule energy is too high. This error occurred in subroutine Deletion on step ZZZ." (Please find my simulations attached.)
I looked in the Forum whether others had this problem already and found the following topic: cassandra.nd.edu/index.php/forum/faq/121...oo-high?limitstart=0
I tried to use the suggested modification to the source code but it also resulted in the above mentioned error.
Could you please help me with this? I am not entirely sure of the cause of this error. I have also tried to run simulations with 1000 water molecules as initial configuration. In this case, the error does not occur.
Thank you for your help in advance.
Best regards,
Máté
In the meanwhile I tried to run the simulations with different initial configurations. For example I tried to run simulations with 150 TCP molecules in the framework as initial configuration. I created this starting configuration two ways:
1. by letting Cassandra create the 150 TCPs randomly (make_config)
2. Run a NVT simulation with 500 000 MC steps for 150 randomly created TCPs in the framework
Unfortunately, when I tried to use these initial configurations I got the following error message: "Attempted to delete molecule XXX of species YYY but the molecule energy is too high. This error occurred in subroutine Deletion on step ZZZ." (Please find my simulations attached.)
I looked in the Forum whether others had this problem already and found the following topic: cassandra.nd.edu/index.php/forum/faq/121...oo-high?limitstart=0
I tried to use the suggested modification to the source code but it also resulted in the above mentioned error.
Could you please help me with this? I am not entirely sure of the cause of this error. I have also tried to run simulations with 1000 water molecules as initial configuration. In this case, the error does not occur.
Thank you for your help in advance.
Best regards,
Máté
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