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!
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)trainset.in I found some quotes are in Datasets/silica/trainset.in.
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?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!