OK, I sorted out what is happening although the symptoms were no not so
obvious!
Pwscf now reduces the cell paremeters and computes a length to multiply
them by, so xtalopt is finding the wrong volume. Thus the result would be
out of range. So for example:
PWSCF output now shows:
celldm(1)= 3.498840 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.276521 -0.167053 -0.156289 )
a(2) = ( -0.172203 2.690797 -0.058968 )
a(3) = ( 0.068258 -0.097907 2.161361 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 0.787140 0.049879 -0.022599 )
b(2) = ( 0.050990 0.375237 0.015387 )
b(3) = ( 0.058310 0.013844 0.461457 )
and there is no way now to set celldm(1)=1 like before. Now pwscf crashes
with an error if you try to set celldm=1 as well as 3x3 cell axes.
so structure.state now shows:
history\cells\1\00=0.675505553217
history\cells\1\01=-0.088400605381
history\cells\1\02=-0.082704544153
history\cells\1\10=-0.091125866931
history\cells\1\11=1.423907884069
history\cells\1\12=-0.031204509336
history\cells\1\20=0.036120563666
history\cells\1\21=-0.051810132539
history\cells\1\22=1.143742529897
alat is fixed by pwscf at the beginning of the run:
lattice parameter (alat) = 3.4988 a.u.
I do not know how these relate to the cell parameters shown in xtal.out .
Very messed up!
Ron
---
Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rco...@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727
On Tue, Jul 28, 2015 at 8:40 AM, David Lonie <david.lo...@kitware.com>
wrote:
> I replied from my other account, but it didn't seem to go to the list?
> Here's my reply for the archives:
>
> On Mon, Jul 27, 2015 at 5:28 PM, Cohen, Ronald <rco...@carnegiescience.edu
> > wrote:
>
>> Actually, still having problems. The attached example shows what seems to
>> me an OK run, and obabel digests it fine, but for some reason xtalopt
>> doesn't take it and generates a new random structure instead. It doesn't
>> show up as a failure (in fact none of the runs do--even the obvious
>> failures. xtalopt just keeps going generating new structures like the
>> attached snapshot shows. Maybe something is wrong with my build, though
>> everything seemed OK. I am running on a new machine. Thanks for any help!
>>
>
> It looks like the parsers should still work for that file (at least for
> the energy terms that XtalOpt needs).
>
> I suspect that the candidate structures are being read in correctly, but
> are then failing some constraint set in XtalOpt (cell length, volume,
> angles, minimum interatomic distance, etc), getting kicked out, and
> replaced with new random structures, as seen in the screenshot. Do these
> rejected structures violate any of the configured cell constraints?
>
> Also, are you running on mac/linux or windows? XtalOpt will print a lot of
> information to stdout about these failed structures. On linux/mac, try
> starting avogadro from a terminal and watch the output for messages about
> rejected structures. On windows, just run avogadro normally, but run
> DebugView[1] at the same time to see the output. This should give a clearer
> idea of why the structures are being replaced.
>
> Hope this helps,
> Dave
>
> [1] https://technet.microsoft.com/en-us/Library/bb896647.aspx
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Avogadro-Discuss mailing list
> Avogadro-Discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
>
>
------------------------------------------------------------------------------
_______________________________________________
Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
