Hello,
I have a question on making “bonds” in data file.
Current syntax of “bonds” section is “ID type atom1 atom2”.
If I use atom-style “full”, I have molecule-ID.
So I think there is a way to use molecule-ID or group-ID instead of each atom to define a bond.
Could anyone let me know please?
e.g.,
according the syntax of “bonds” section,
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
–> using molecule-ID or group-ID, (is this possible??)
1 harmonic molecule-A # which means all atoms in molecule-A are bonded via harmonic.
2 harmonic molecule-A molecule-B # which means all atoms in molecule-A are bonded via harmonic with all atoms in molecule-B
3 harmonic group-C # which means all atoms in group-C are bonded via harmonic.
Hello,
hello edward,
I have a question on making "bonds" in data file.
Current syntax of "bonds" section is "ID type atom1 atom2".
If I use atom-style "full", I have molecule-ID.
So I think there is a way to use molecule-ID or group-ID instead of each
atom to define a bond.
no.
Could anyone let me know please?
e.g.,
according the syntax of "bonds" section,
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
--> using molecule-ID or group-ID, (is this possible??)
1 harmonic molecule-A # which means all atoms in molecule-A are bonded
via harmonic.
this doesn't make any sense.
the selection of what functional form is used to compute
the bonded form is done via the "bond_style" command.
the bond type defines which parameter set is being used.
2 harmonic molecule-A molecule-B # which means all atoms in molecule-A
are bonded via harmonic with all atoms in molecule-B
3 harmonic group-C # which means all atoms in group-C are bonded via
harmonic.
do you really want to have a bond between _any_ atom in molecule A
and _every other_ atom in molecul A?
in that case, it should be easy to write a script or short program to
generate those. same for all other permutations.
axel.