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
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
On Tue, Jul 28, 2015 at 8:40 AM, David Lonie david.lonie@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 <rcohen@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] DebugView - Sysinternals | Microsoft Learn
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