Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output

[Cohen, R. <rc...@ca...>]

Further info:

from the pwscf input descriptions:

celldm(i), i=1,6REAL

Specify either these OR A,B,C,cosAB,cosBC,cosAC NOT both.
Only needed values (depending on "ibrav") must be specified
alat = celldm(1) is the lattice parameter "a" (in BOHR)
If ibrav=0, only celldm(1) is used if present;
cell vectors are read from card CELL_PARAMETERS

It also says:

'bohr'/'angstrom': lattice vectors in bohr radii / angstrom.
   In this case the lattice parameter alat = sqrt(v1*v1).


which doesn't make any sense.

Ron

---
Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rc...@ca...
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
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On Wed, Jul 29, 2015 at 4:50 PM, Cohen, Ronald
<rc...@ca...> wrote:
> 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
> rc...@ca...
> 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 <dav...@ki...>
> 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
>> <rc...@ca...> 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
>>
>>
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