Hi everyone,
I am having trouble with getting deleted bonds to turn back on again after minimization. Here is the log from the delete_bonds commands:
delete_bonds all bond 3
960 total bonds, 870 turned on, 90 turned off
680 total angles, 680 turned on, 0 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
.
.
…minimize…
.
.
#undo delete_bonds
delete_bonds all bond 3 undo
960 total bonds, 870 turned on, 90 turned off
680 total angles, 680 turned on, 0 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
As you can see from the log, the bonds are still turned off (the 90 bonds) after I’ve undone the original delete_ bonds command. Any ideas what might be wrong and how to fix this?
Thanks,
Cam Tran
Hi everyone,
I am having trouble with getting deleted bonds to turn back on again after
minimization. Here is the log from the delete_bonds commands:
delete_bonds all bond 3
960 total bonds, 870 turned on, 90 turned off
680 total angles, 680 turned on, 0 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
.
.
...minimize....
.
.
#undo delete_bonds
delete_bonds all bond 3 undo
960 total bonds, 870 turned on, 90 turned off
680 total angles, 680 turned on, 0 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
As you can see from the log, the bonds are still turned off (the 90 bonds)
after I've undone the original delete_ bonds command. Any ideas what might
be wrong and how to fix this?
hard to say, if this is a logic bug or a desired feature, but your
second command is not correct with the current implementation.
since disabled bonds have a negative type, you would have to use the command:
delete_bonds all bond -3 undo
to do what you want. the type 3 bonds simply don't match.
axel.
hard to say, if this is a logic bug or a desired feature, but your
second command is not correct with the current implementation.
since disabled bonds have a negative type, you would have to use the command:
delete_bonds all bond -3 undo
to do what you want. the type 3 bonds simply don’t match.
well, that’s counter-intuitive. Not sure why we
did it that way.
I just changed delete bonds, to always take positive types as
an argument, but use the “undo” keyword to mean
flip a negative to a positive for those types.
I also added a wildcard option to the type arg,
so you can specify 1*3 if you want to act on all
interactions of type = 1,2,3. Similar to the pair_coeff
command.
Will be in the next patch.
Steve
Thank you Steve and Axel.
I was able to figure it out after careful reading of the doc page, but yes, it was a bit counter-intuitive. I appreciate both of your help and input. The wildcard option does save me some time as well.
Thanks again,
Cam
hard to say, if this is a logic bug or a desired feature, but your
second command is not correct with the current implementation.
since disabled bonds have a negative type, you would have to use the command:
delete_bonds all bond -3 undo
to do what you want. the type 3 bonds simply don’t match.
well, that’s counter-intuitive. Not sure why we
did it that way.
I just changed delete bonds, to always take positive types as
an argument, but use the “undo” keyword to mean
flip a negative to a positive for those types.
I also added a wildcard option to the type arg,
so you can specify 1*3 if you want to act on all
interactions of type = 1,2,3. Similar to the pair_coeff
command.
Will be in the next patch.
Steve