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Description
Dear developer,
Hi, I found this very interesting program recently and am trying to understand how to use this to make a revised reaxff parameters.
To do so, could you explain more about some details of geo, params, and trainset.in files?
geo
I'm not familiar with BIOGRF/XTLGRF format but seems like it has x y z cartesian coordinate and charge information.
(HETATM 1 Si 40.00000 40.00000 39.23957 Si 1 1 0.16252)
- Is the charge here is from some general force-field? And is this charge actually matter for parameterizing reaxFF?
- Also, it has ENERGY (kcal/mol) value and which method is used to calculate this energy value?
- Is this something like a atomization energy? and are those values are used somewhere?
- Is there any software for generating BIOGRF format from like mol2 formated file? will be great if you share the way how to generate geo file...
trainset.in
I found some quotes are in Datasets/silica/trainset.in.
- For ENERGY section, for example,
30.0 + geo5 /1 - si1 /1 -162.30,
30.0 seems like meaning the weight and if this weight values are greater, reaxFF parameters are more dependent to this reaction energies. Is this right? Please correct me if I understood wrongly. Is -162.30 is kcal/mol unit and from other method like DFT? - For CHARGE section, e.g.,
geo8 0.1 1 -0.597, geo8 seems to indicate DESCRP in geo file, 0.1 is the weight, and 1 is the atom number 1 in geo8 (Oxygen in this case) and -0.597 seems like a desired charge. Is this charge from the other calculation like DFT or MP2?
params
I found some descriptions inside Datasets/disulfide/params but this param is really hard to figure it out...
for 2 1 10 0.0050 1.5000 2.5000 ! C-Atom,
2 seems like indicating something like the characteristics of the row. For example 3 seems like for bonding, 5 seems like Angle, etc.
1 seems like indicating the element, Carbon in this case.
I have no idea what 10 means.
0.0050 seems like a weight, 1.5000 and 2.5000 seems like a range of something but again have no idea... Could you please explain details of these parameters?
If I understand the things above, it might be a great help to start using JAX-ReaxFF, although it seems like making a real-working reaxFF parameter might be really a hard work....
Thanks again for the hard work!