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