Proposal for storing bonding information #23
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Topology/README.md
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| For metadata, there are a few pre-defined keys with strict meanings: | ||
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| * `bond_type` can take values `single`, `double`, `triple` [to replace -- this is just an example], only suitable for connections involving pairs of atoms |
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Angle and torsions would need to be handled in a similar way
bond_type defined as is may not be necessary. Single, double, triple ... bonds are defined through the set of parameters associated with each atom type
Topology/README.md
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| For metadata, there are a few pre-defined keys with strict meanings: | ||
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| * `bond_type` can take values `single`, `double`, `triple` [to replace -- this is just an example], only suitable for connections involving pairs of atoms |
There was a problem hiding this comment.
Angle and torsions would need to be handled in a similar way
bond_type defined as is may not be necessary. Single, double, triple ... bonds are defined through the set of parameters associated with each atom type
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Agreed -- I don't know if bond_type specifically is necessary, I included it as an example. I think some pre-defined keys might be useful for GUI/visualization though.
Topology/README.md
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| Each connection is defined as: | ||
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| * `indices`, an ordered list of length `N` of atomic indexes defining the connection | ||
| * `images`, (optional, only relevant if a unit cell lattice is defined) an ordered list of length `3N` describing the periodic image of the connected atom -- by default, this is assumed to be (0,0,0), meaning that the connected atom is in the origin image, and first index is set to (0,0,0) by convention |
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Why not a list of lists like for gemoetry and unit_cell?
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I'd like that -- it'd make it a lot more human readable. I'm not sure if it'd have consequences for file size/loading time for large systems though.
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Right, but geometry is currently specified as a list of lists, and the same issue applies there...
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I agree it should be consistent with geometry, I didn't realize this was list of lists.
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Looks good |
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| For metadata, there are a few pre-defined keys with strict meanings: | ||
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| * `bond_type` can take values `single`, `double`, `triple` [to replace -- this is just an example], only suitable for connections involving pairs of atoms, this is useful for GUI/visualization tools |
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What about order, and use an integer rather than a string, or are there other types being envisaged?
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Order sounds sensible! bond_type was just an example to get the conversation started: some pre-defined keys would be good, I'm (personally) agnostic as to what these keys should be.
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But order and an integer value sounds good.
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Sounds like geometry should be changed following discussions from yesterday. I can make a pull request.
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Any real objection to adding bond_types as floats to allow slightly more flexibility for say aromatic compounds.
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Added #28 to make these more uniform |
1. Change field `masses` to mass of molecule to mass of atoms. I think this was a typo. 2. Add fields `num_protons`, `num_electrons`, and `basis`. The ghost and dummy atoms can be constructed with the appropriate selection of these fields (plus `masses`)
1. Add examples for symbols, geometry, name, multiplicity, masses, num_protons, num_electrons, basis, comment, fragments, fragment_charges, and fragment_multiplicities,
Add more specifications for each atom
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@mkhorton The schema layout has changed quite a bit since this PR, apologies! If you can supply 1-2 JSON examples I would be more than happy to work on incorporating this. |
This is following the 'big system' approach of large arrays containing information for all atoms.