Format of the geo file for parameterization
For each structure that is referred to in the trainset.in file, there must be a corresponding entry in the geo file. The format of a structure in the geo file is shown below (for antimony trichloride). This example was taken from ~jkua/reac/sbcl/geo
BIOGRF 200
DESCRP sbcl3_24.op
REMARK
RUTYPE NORMAL RUN
FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)
HETATM 1 Sb 40.41155 39.64213 39.99990 Sb 1 1 0.00000
HETATM 2 Cl 38.84005 39.61667 41.82186 Cl 1 1 0.00000
HETATM 3 Cl 40.90611 41.99579 40.00002 Cl 1 1 0.00000
HETATM 4 Cl 38.84041 39.61663 38.17845 Cl 1 1 0.00000
FORMAT CONECT (a6,12i6)
CONECT 1 2 3 4
CONECT 2 1
CONECT 3 1
CONECT 4 1
UNIT ENERGY kcal
ENERGY -200.129440
END
There are two important things in the file above.
(1) The name in DESCRP must be exactly the same as used in the trainset.in file.
(2) Formatting is crucial. You must have the right number of spaces in between columns in the geometry (the four lines starting with HETATM).
To generate a geo structure entry from your Jaguar file, you can use the jag2geo script that will give you everything in the right format. (You must still change the DESCRP.) You will notice after using the script that the actual number for the energy and the CONECT lines are not important when first creating the geo file. ReaxFF will put these in when it goes through the parameterization.
To add a constraint in your structure, replace the line RUTYPE NORMAL RUN with
# At1 At2 R12 Force1 Force2 dR12/dIter(MD) Start (MD) End (MD)
BOND RESTRAINT 1 2 2.6093 2500.00 1.0000 0.0000000 0 0
For example, the file below has one of the Sb-Cl bonds (atoms 1 and 2) stretched to 2.6 Angstroms. The typical Force restraint is 2500 so you can stick to this default value. Note that DESCRP is also different.
BIOGRF 200
DESCRP sbcl3_26
REMARK
# At1 At2 R12 Force1 Force2 dR12/dIter(MD) Start (MD) End (MD)
BOND RESTRAINT 1 2 2.6093 2500.00 1.0000 0.0000000 0 0
FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)
HETATM 1 Sb 39.69302 39.63708 39.70387 Sb 1 1 0.00000
HETATM 2 Cl 39.70040 39.63753 42.30964 Cl 1 1 0.00000
HETATM 3 Cl 42.06078 39.63870 39.35370 Cl 1 1 0.00000
HETATM 4 Cl 39.29305 41.97019 39.35372 Cl 1 1 0.00000
FORMAT CONECT (a6,12i6)
CONECT 1 2 3 4
CONECT 2 1
CONECT 3 1
CONECT 4 1
UNIT ENERGY kcal
ENERGY -195.144132
END