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

[David Lonie]

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
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