[Wien] Slab convergence
Lukasz Plucinski
pluto at physics.ucdavis.edu
Tue Sep 14 12:49:39 CEST 2010
Dear Laurence,
I was able to compile entire program using Portland compiler with
generic options. Now iterations work, however, neither Au20 nor Fe1Au20
slabs didn't converge yet (sp far I got down to 0.0016 in energy for
Au20 slab). For simple cases there is no problem with convergence, I
tested for bulk Au (not complex) and bulk GaAs (complex).
So far I am happy with this, and I would like to thank you for your
supporting and motivating comments last couple of days. At the moment I
am using old 2.8 GHz P4 CPU (released in 2002), maybe I will order a new
computer, and then compile things properly. Is there any preference for
the CPU type nowadays ? For example I can see various Intel i7 and i5
priced around 200 Euro. Are some Linux systems more preferable than others ?
lapw0 and lapw1 produced by Portland compiler are very slow, and instead
of them I use precompiled executables (especially lapw0 was very very
slow :) ).
At this point I can concentrate again on optimizing the convergence. You
have mentioned 2 things:
- using TEMPS instead of TETRA with 0.0018 temperature factor,
- using iterative mode,
Could you comment if and how they may help the convergence ?
Do you think changing cutoff from -6 to -8 Ry could help the convergence
when Fe atom is involved ?
Regards,
Lukasz
On 9/13/2010 6:58 PM, Laurence Marks wrote:
> -noHinv (not -nohns, they are VERY different)!
>
> A SIGSEV is a moderately serious problem, and might be in the
> executables you are using -- I don't know and I believe Peter Blaha is
> at a conference. I would strongly suggest getting help with the
> compilation, it is not that hard and I think you have some people at
> Davis who know what they are doing.
>
> On Mon, Sep 13, 2010 at 11:53 AM, Lukasz Plucinski
> <pluto at physics.ucdavis.edu> wrote:
>> Dear Laurence,
>>
>> Thank you for your support.
>>
>> Before starting another test I always delete all files in the "case"
>> directory, leaving only the case.struct file there.
>>
>> I would really like to avoid compiling the program and I try to use
>> executables which are also available. I am not really interested in
>> optimized performance of the system, and my 20ML slab should calculate
>> within several hours on my machine if all works fine. I am using Fedora
>> Linux, and Wien2k_08 compiled executables were working fine on this system.
>>
>> But maybe compiling will be mandatory at the end, which for me probably
>> means that I will have to get some support from the IT group in our
>> institute. But before I start organizing this I would like to further
>> explore the option with compiled executables :)
>>
>> At the moment the problem seems to be lapw2c (bulk Au calculation, which
>> works, does not use the -c complex option). The history of my last try with
>> -it and -nohns (as you suggested) options is below. Here is the
>> case.dayfile:
>>
>> Calculating Au20_ver2 in /local/WORK/Au20_ver2
>> on iff187 with PID 3798
>> using WIEN2k_10.1 (Release 7/6/2010) in /local/WIEN
>>
>> start (Mon Sep 13 18:20:57 CEST 2010) with lapw0 (40/99 to go)
>>
>> cycle 1 (Mon Sep 13 18:20:58 CEST 2010) (40/99 to go)
>>
>>> lapw0 (18:20:58) 82.578u 1.729s 1:25.89 98.1% 0+0k 0+16856io
>>> 0pf+0w
>> moving Au20_ver2.vectorup to Au20_ver2.vectorup.old
>> moving Au20_ver2.vectordn to Au20_ver2.vectordn.old
>>> lapw1 -it -c -up -nohns (18:22:24) 115.475u 4.607s 2:05.42 95.7%
>>> 0+0k 0+156080io 0pf+0w
>>> lapw1 -it -c -dn -nohns (18:24:29) 96.951u 3.882s 1:42.15 98.7% 0+0k
>>> 0+153000io 0pf+0w
>>> lapw2 -c -up (18:26:11) 0.274u 0.108s 0:00.38 97.3% 0+0k
>>> 0+1848io 0pf+0w
>> error: command /local/WIEN/lapw2c uplapw2.def failed
>>
>>> stop error
>>
>>
>> and the STDOUT:
>>
>> File: STDOUT Line 1 Col 0 144 bytes
>> 100%
>> LAPW0 END
>> LAPW1 END
>> LAPW1 END
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>
>> Stack trace terminated abnormally.
>>
>>> stop error
>>
>> Regards,
>> Lukasz
>>
>>
>>
>> On 9/13/2010 5:48 PM, Laurence Marks wrote:
>>> 1. Do "rm *.rec*" -- old files with k-vectors in them might be a problem.
>>> 2. Are you using openmpi? This can be an issue.
>>> 3. Did you restart in a fresh directory from just your struct file and
>>> redo init_lapw? Safest.
>>>
>>> On Mon, Sep 13, 2010 at 10:41 AM, Lukasz Plucinski
>>> <pluto at physics.ucdavis.edu> wrote:
>>>> Dear Laurence,
>>>>
>>>> Thank you for the rapid response. Indeed I deleted all files in Wien root
>>>> directory, and started from there.
>>>>
>>>> Now the calculation for bulk Au runs, and the R0 warning is gone, when
>>>> the
>>>> number is 100 times smaller (it was 0.0001, and now its 0.000001 for Au).
>>>> Also struct editor keeps setting RMT as 2.5, which is too small for bulk
>>>> Au.
>>>>
>>>> The calculation for 20ML Au slab (which has worked before) gets stuck at
>>>> first LAPW2 in SCF cycle -- LAPW1 ends after 1 or 2 minutes, and LAPW2
>>>> keeps
>>>> running 20 or more minutes, then I kill it (because I assume it will
>>>> never
>>>> end).
>>>>
>>>> I suspect things are still not properly installed, however, this does not
>>>> explain why bulk Au calculation works fine...
>>>>
>>>> Maybe you could suggest some simple tests I could do ?
>>>>
>>>> Regards,
>>>> Lukasz
>>>>
>>>>
>>>>
>>>>
>>>> On 9/13/2010 3:05 PM, Laurence Marks wrote:
>>>>> Pay attention to the warning about R0 and change this in the struct
>>>>> file. (Previously it was possible to run calculations with too large a
>>>>> value and not know.) Apart from this it is hard to know and rerunning
>>>>> siteconfig is safer.
>>>>>
>>>>> On Mon, Sep 13, 2010 at 7:36 AM, Lukasz Plucinski
>>>>> <pluto at physics.ucdavis.edu> wrote:
>>>>>> Hello,
>>>>>>
>>>>>> I copied newest version of Wien2k (previously I was using version 08).
>>>>>> I
>>>>>> would really prefer to avoid compiling a new version, thus I just
>>>>>> copied
>>>>>> (overwritten) the binaries (executables) into the root Wien directory.
>>>>>> However, not everything seems to work now...
>>>>>>
>>>>>> First I tried to calculate bulk Au as a test. Automatic RMT procedure
>>>>>> has
>>>>>> determined the RMT as 2.5 although it should be around 2.72... I don't
>>>>>> understand why but this does not really change much.
>>>>>>
>>>>>> First warning appears when running lstart:
>>>>>>
>>>>>> WARNING: R0 for atom 1 Z= 79.00 too big
>>>>>>
>>>>>> There is no problems with leaking charge:
>>>>>>
>>>>>> TOTAL CORE-CHARGE: 54.000001
>>>>>> TOTAL CORE-CHARGE INSIDE SPHERE: 53.999826
>>>>>> TOTAL CORE-CHARGE OUTSIDE SPHERE: 0.000175
>>>>>>
>>>>>> Then the rest of initialization goes fine and there is no problem with
>>>>>> convergence. I can also calculate the band structure, however, not the
>>>>>> option of partial charges. Trying to calculate partial charges gives
>>>>>> the
>>>>>> following error:
>>>>>>
>>>>>> Commandline: x lapw2 -band -qtl -up
>>>>>> Program input is: ""
>>>>>> forrtl: severe (256): unformatted I/O to unit open for formatted
>>>>>> transfers,
>>>>>> uni
>>>>>> t 15, file /local/WORK/Au-bulk-no-SO/Au-bulk-no-SO.tmpup
>>>>>> Image PC Routine Line Source
>>>>>> lapw2 082CDBED Unknown Unknown Unknown
>>>>>> lapw2 082CD165 Unknown Unknown Unknown
>>>>>> lapw2 08288C98 Unknown Unknown Unknown
>>>>>> lapw2 08252AFA Unknown Unknown Unknown
>>>>>> lapw2 0825241B Unknown Unknown Unknown
>>>>>> lapw2 08279804 Unknown Unknown Unknown
>>>>>> lapw2 080899EE outp_ 207 outp.f
>>>>>> lapw2 0807B3AF l2main_ 1710
>>>>>> l2main_tmp_.F
>>>>>> lapw2 08083AFB MAIN__ 545
>>>>>> lapw2_tmp_.F
>>>>>> lapw2 080482A1 Unknown Unknown Unknown
>>>>>> lapw2 082D8E30 Unknown Unknown Unknown
>>>>>> lapw2 08048161 Unknown Unknown Unknown
>>>>>> 0.324u 0.097s 0:00.42 97.6% 0+0k 0+2224io 0pf+0w
>>>>>>
>>>>>> Doing all this on my Fe1Au20 slab gives the same "WARNING: R0 for atom
>>>>>> 1
>>>>>> Z= 79.00 too big" warning, and then during SCF run the programs gets
>>>>>> stuck
>>>>>> on a first LAPW2, it does not give the error, but the LAPW2 continues
>>>>>> forever... Thus probably there is something wrong with my LAPW2, or
>>>>>> perhaps
>>>>>> my Wien2k_10 is not properly installed.
>>>>>>
>>>>>> I will keep working to solve this, but I am sure your suggestions will
>>>>>> help.
>>>>>>
>>>>>> Regards,
>>>>>> Lukasz
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 9/12/2010 3:37 PM, Laurence Marks wrote:
>>>>>>> N.B., of course when you compare to the number of k-points for bulk Au
>>>>>>> remember to use the primitive cell volume.
>>>>>>>
>>>>>>> On Sun, Sep 12, 2010 at 8:21 AM, Laurence Marks
>>>>>>> <L-marks at northwestern.edu> wrote:
>>>>>>>> Some comments:
>>>>>>>>
>>>>>>>> 1. 100 k-points for a surface is a lot. What I suggest you do is
>>>>>>>> determine how many k-points you need per reciprocal nm^3 (i.e. the
>>>>>>>> multiple of the 3 numbers after "div:" in line 1 of case.klist and
>>>>>>>> the
>>>>>>>> cell volume) for a bulk calculation then use the same density for a
>>>>>>>> surface.
>>>>>>>>
>>>>>>>> 2. Are you using TETRA? I recommend TEMPS for surfaces with a
>>>>>>>> temperature factor of 0.0018 (room temperature).
>>>>>>>>
>>>>>>>> 3. DO NOT REDUCE THE MIXING FACTOR (better called MIXING GREED)
>>>>>>>> unless
>>>>>>>> you understand what you are doing. For old PRATT and BROYD methods
>>>>>>>> this was correct, for MSEC1 it is fundamentally wrong. Too large a
>>>>>>>> mixing greed (say 0.5) is being too greedy, but the algorithm in fact
>>>>>>>> prevents this from happening. To small a greed and the algorithm will
>>>>>>>> starve to death.
>>>>>>>>
>>>>>>>> 4. In 98% of cases where the calculation does not converge this is
>>>>>>>> because something is wrong in the physics of the model, i.e. bad
>>>>>>>> functional or incorrect structure. Possibly the Fe atom is too far
>>>>>>>> from the surface -- have you set FOR in case.in2 and looked at how
>>>>>>>> big
>>>>>>>> these are? With care, you can run a minimization with something like
>>>>>>>> -fc 4 -ec 0.001 at first, then improve these later.
>>>>>>>>
>>>>>>>> 5. When you say it is not converging what do you really mean? The
>>>>>>>> default -ec 0.0001 is very strict for a surface (with incorrect
>>>>>>>> positions), realise that the energy convergence should scale as
>>>>>>>> something like the number of atoms (or the square root of this).
>>>>>>>>
>>>>>>>> 6. Are you using 10.1 and iterative mode? 10.1 is noticeably better
>>>>>>>> and I prefer to use -noHinv.
>>>>>>>>
>>>>>>>> On Sun, Sep 12, 2010 at 7:26 AM, Lukasz Plucinski
>>>>>>>> <pluto at physics.ucdavis.edu> wrote:
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> I am trying to calculate 1ML of Fe on top of Au(001).
>>>>>>>>>
>>>>>>>>> It was no problem to calculate 20ML slab of Au(001), it converged
>>>>>>>>> after
>>>>>>>>> 37
>>>>>>>>> iterations with mixing 0.1, 100k-points and all other standard
>>>>>>>>> settings,
>>>>>>>>> also using "spin-polarized" calculation mode. I use 50 A of the unit
>>>>>>>>> cell
>>>>>>>>> dimension, to have appropriate amount of vacuum.
>>>>>>>>>
>>>>>>>>> However, when I put 1 Fe atom on top of one side of the slab the
>>>>>>>>> calculation
>>>>>>>>> didn't converge after 100 iterations (I did couple of trials). I
>>>>>>>>> also
>>>>>>>>> tried
>>>>>>>>> to increase the cutoff to -8 Ry, and the calculation is running now,
>>>>>>>>> however, no convergence indications after 35 iterations.
>>>>>>>>>
>>>>>>>>> My slab is not relaxed, and the distance between Fe and Au (3.295
>>>>>>>>> au)
>>>>>>>>> is
>>>>>>>>> taken from the old publication of Freeman JMMM 75, 201 (1988).
>>>>>>>>>
>>>>>>>>> Automatic RMT distance procedure has put all RTM to 2.5, however,
>>>>>>>>> this
>>>>>>>>> way
>>>>>>>>> there is a lot of space between Au atoms. I think its better to use
>>>>>>>>> 2.72
>>>>>>>>> for
>>>>>>>>> Au atoms and 2.34 for Fe atom -- is there any problem with this ?
>>>>>>>>> Neither
>>>>>>>>> setting helps the convergence...
>>>>>>>>>
>>>>>>>>> Maybe I could decrease the amount of k-points to have faster
>>>>>>>>> iterations
>>>>>>>>> with
>>>>>>>>> even lower mixing parameter ?
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>> Lukasz
>>>>>>>>> _______________________________________________
>>>>>>>>> Wien mailing list
>>>>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Laurence Marks
>>>>>>>> Department of Materials Science and Engineering
>>>>>>>> MSE Rm 2036 Cook Hall
>>>>>>>> 2220 N Campus Drive
>>>>>>>> Northwestern University
>>>>>>>> Evanston, IL 60208, USA
>>>>>>>> Tel: (847) 491-3996 Fax: (847) 491-7820
>>>>>>>> email: L-marks at northwestern dot edu
>>>>>>>> Web: www.numis.northwestern.edu
>>>>>>>> Chair, Commission on Electron Crystallography of IUCR
>>>>>>>> www.numis.northwestern.edu/
>>>>>>>> Electron crystallography is the branch of science that uses electron
>>>>>>>> scattering and imaging to study the structure of matter.
>>>>>>>>
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>>>
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