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General Questions and Answers / Re: Manual implementation of CLAYFF
« on: May 4, 2021, 17:11 »
Here is the general description of the system and the last two tag files.
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General Questions and Answers / Manual implementation of CLAYFF
« on: May 4, 2021, 17:10 »
I've been working for some time attempting to construct the CLAY force field (Cygan, 2004) using the potentials/Coulomb solvers available in ATK. My ultimate goal is to measure diffusion of water through a mesoporous silica nanopore (MSN). Per another question on the forum about creating gaps in the periodic images, the z lattice parameter is 30 Angstrom longer than the system (made up of water and the pore).
I'm running into several issues. First, I can't actually get a simulation to run without a few atoms breaking bonds and shooting off into the space beyond the defined lattice. Second, occasionally when it IS running, it stops and gives me the error or "Particle leaving simulation area."
I've checked the interatomic distances and charge balance several times.
I'm not going to describe the FF, etc, in too much detail here. It's all in the input file. I've included the input file and the tag files that go along with it. The FF is made up of the particle definitions, LJ spline potentials, and the SPME Coulomb solver. CLAY would typically involve several more particle types, but I only defined what I needed. The six particle types are the silicon in the bulk, the oxygen in the bulk(Ob), the hydroxyl oxygen attached to the pore surface(Ox), the hydroxyl hydrogen(Hx), water oxygen(Ow), and water hydrogen(Hw)
Can anyone reproduce what I'm seeing and have any advice on how to fix it?
I'm running into several issues. First, I can't actually get a simulation to run without a few atoms breaking bonds and shooting off into the space beyond the defined lattice. Second, occasionally when it IS running, it stops and gives me the error or "Particle leaving simulation area."
I've checked the interatomic distances and charge balance several times.
I'm not going to describe the FF, etc, in too much detail here. It's all in the input file. I've included the input file and the tag files that go along with it. The FF is made up of the particle definitions, LJ spline potentials, and the SPME Coulomb solver. CLAY would typically involve several more particle types, but I only defined what I needed. The six particle types are the silicon in the bulk, the oxygen in the bulk(Ob), the hydroxyl oxygen attached to the pore surface(Ox), the hydroxyl hydrogen(Hx), water oxygen(Ow), and water hydrogen(Hw)
Can anyone reproduce what I'm seeing and have any advice on how to fix it?
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General Questions and Answers / Re: tag_data formatting
« on: August 25, 2020, 22:27 »
Thank you for the help. I managed to get past that error.
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General Questions and Answers / tag_data formatting
« on: August 20, 2020, 03:44 »
Hello,
I've manually created my own force field (potential). In order for this manually-constructed potential to work, I need to assign tags to two different types of oxygen atoms. I'm attempting to add this dictionary to the BulkConfiguration() class using the tag_data argument. I've constructed several dictionaries attempting to do this, but each time I receive:
NL.ComputerScienceUtilities.Exceptions.NLValueError: All tag data values must be sets of integers.
I've checked and rechecked, and my script-created dictionaries only include data as sets of integer values.
The dictionaries I've constructed include:
{"tag1": [list of indices for tag1], etc...}
{"tag1": individual index as a single integer, etc...}
as well as other variations and reversed order in terms of key:value pairs.
Could someone please provide a more detailed description of what the tag_data argument should actually look like? I did not find an example of this for individual atoms in the bulkConfiguration class.
Thank you. [/list]
I've manually created my own force field (potential). In order for this manually-constructed potential to work, I need to assign tags to two different types of oxygen atoms. I'm attempting to add this dictionary to the BulkConfiguration() class using the tag_data argument. I've constructed several dictionaries attempting to do this, but each time I receive:
NL.ComputerScienceUtilities.Exceptions.NLValueError: All tag data values must be sets of integers.
I've checked and rechecked, and my script-created dictionaries only include data as sets of integer values.
The dictionaries I've constructed include:
{"tag1": [list of indices for tag1], etc...}
{"tag1": individual index as a single integer, etc...}
as well as other variations and reversed order in terms of key:value pairs.
Could someone please provide a more detailed description of what the tag_data argument should actually look like? I did not find an example of this for individual atoms in the bulkConfiguration class.
Thank you. [/list]
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