[XtalOpt-devel] controlling the keyword in GULP and Xtalopt

[Wei Lai]

Dear David,

Thanks for your reply. I am on windows and I'd like to have the flag of "1
1 0 1 1 1". I can wait for it.

Regards, Wei


On Sat, Jun 16, 2012 at 9:23 AM, David Lonie <loniedavid at gmail.com> wrote:

> On Fri, Jun 15, 2012 at 6:53 PM, Wei Lai <laiwei at msu.edu> wrote:
> > I would like to add additional flags after the coordinates to obtain the
> > following:
> > La 0.2 0.6 0.7 3 1 0 1 1 1
> > La 0.1 0.2 0.3 3 1 0 1 1 1
> >
> > Is there a way to do this?
>
> This is not currently implemented. If you've compiled XtalOpt
> yourself, you can apply the attached patch to add this functionality:
>
> cd path/to/xtalopt/source/code/ # Usually ~/src/xtalopt/
> patch -p1 < coordFlags.diff
>
> then build (make) and install (make install) again and use the keyword
> "%coordsFracCustom%". I ran a test and got:
>
> O -0.0689392 0.278319 0.0313129 3 1 0 1 1 1
> N -0.18792 -0.0825675 9.80208e-05 3 1 0 1 1 1
> N 0.204552 0.0154757 -0.00768081 3 1 0 1 1 1
> C -0.0198324 0.0801368 0.00900635 3 1 0 1 1 1
> H -0.152938 -0.242758 -0.0177075 3 1 0 1 1 1
> H -0.345974 -0.0365482 0.0118565 3 1 0 1 1 1
> H 0.322753 0.130477 -0.00128565 3 1 0 1 1 1
> H 0.248298 -0.142535 -0.0255998 3 1 0 1 1 1
> O -0.0689392 0.278319 0.531313 3 1 0 1 1 1
> N -0.18792 -0.0825675 0.500098 3 1 0 1 1 1
> N 0.204552 0.0154757 0.492319 3 1 0 1 1 1
> C -0.0198324 0.0801368 0.509006 3 1 0 1 1 1
> H -0.152938 -0.242758 0.482293 3 1 0 1 1 1
> H -0.345974 -0.0365482 0.511857 3 1 0 1 1 1
> H 0.322753 0.130477 0.498714 3 1 0 1 1 1
> H 0.248298 -0.142535 0.4744 3 1 0 1 1 1
>
> Is this what you needed? If you want to change the flags, edit
> src/xtalopt/xtalopt.cpp and search for "coordsFracCustom". A few lines
> below it, you'll see:
>
>        rep += QString(OpenBabel::etab.GetSymbol(atom->atomicNumber())) + "
> ";
>        rep += QString::number(coords.x()) + " ";
>        rep += QString::number(coords.y()) + " ";
>        rep += QString::number(coords.z()) + " 3 1 0 1 1 1\n";
>
> You can change the flags on the last line to whatever you need them to
> be, then rebuild and reinstall XtalOpt.
>
> If you're on windows, let me know and I'll try to make a new installer
> for you, but it may be a while before I have time.
>
> Hope this helps,
>
> Dave
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmolecules.net/pipermail/xtalopt-devel-openmolecules.net/attachments/20120616/ae6afab0/attachment-0002.htm>