[gpaw-users] about PAW datasets for rare earth elements

Mon Aug 20 11:20:14 CEST 2018

On 08/20/2018 10:13 AM, shijm89 wrote:
> Thank you for your reply.
> I had 1.14 before,
> but after I upgraded the numpy to 1.15.
> still same error occured.

Could you try to insert a print statement right before the failing 
line?  Print the value of "e" and maybe other interesting stuff.

Jens Jørgen

> here are the details about my gpaw
> python-2.7.12            /usr/bin/python
> gpaw-1.4.0 /home/asus/.local/lib/python2.7/site-packages/gpaw/
> ase-3.16.2 /home/asus/.local/lib/python2.7/site-packages/ase/
> numpy-1.15.0 /usr/local/lib/python2.7/dist-packages/numpy/
> scipy-1.0.1 
> /home/asus/mylib/lib/python2.7/site-packages/scipy-1.0.1-py2.7-linux-x86_64.egg/scipy/
> _gpaw /home/asus/.local/lib/python2.7/site-packages/_gpaw.so
> parallel                 /home/asus/.local/bin/gpaw-python
> FFTW                     yes
> scalapack                no
> libvdwxc                 no
> PAW-datasets             1: /usr/local/share/gpaw-setups
>                          2: /usr/share/gpaw-setups
>
> On 08/19/2018 02:16 PM, shijm89 wrote:
>> Dear Jens Jørgen,
>> when I use the command
>> gpaw dataset Pr -P 5s,6s,5p,6p,5d,2.2d,4f,0.4f,G -r 
>> 2.95,2.65,2.30,2.05 -0 5,2.00 -sw -f PBE
>> to generate the PAW data of Pr.
>> A error occured.
>> gpaw/atom/aeatom.py:297: RuntimeWarning: invaild value encountered in 
>> double_scalars
>> ag=np.exp(-(-2 * e)**0.5 * (r_g[gmax - 2]-r_g[gmax -1]))
>
> What version of NumPy do you have?  I have 1.15 and that works OK.
>
> Jens Jørgen
>
>> I tried gpaw 1.3.1, 1.4.0 and 1.4.1b1. Same error occured.
>> Could you kindly give me a hint on this?
>> On 06/13/2018 09:01 AM, shijm89 wrote:
>>> Dear Jens Jørgen
>>> Thank you for your help on my problem before.
>>> Could you kindly give me the experimental PAW datasets?
>>
>> You can generate them by running these commands:
>>
>>    gpaw dataset La -P 5s,6s,5p,6p,5d,3.2d,4f,0.4f,G -r 
>> 2.60,3.05,3.15,2.45 -0 5,2.35 -sw -f PBE
>>    gpaw dataset Ce -P 5s,6s,5p,6p,5d,0.2d,4f,0.7f,G -r 
>> 2.60,3.25,2.60,2.35 -0 5,2.15 -sw -f PBE
>>    gpaw dataset Pr -P 5s,6s,5p,6p,5d,2.2d,4f,0.4f,G -r 
>> 2.95,2.65,2.30,2.05 -0 5,2.00 -sw -f PBE
>>    gpaw dataset Nd -P 5s,6s,5p,6p,5d,3.8d,4f,-0.2f,G -r 
>> 2.80,2.30,2.10,2.15 -0 5,1.90 -sw -f PBE
>>    gpaw dataset Pm -P 5s,6s,5p,6p,5d,1.7d,4f,-0.3f,G -r 
>> 1.95,2.80,2.95,2.25 -0 5,1.95 -sw -f PBE
>>    gpaw dataset Sm -P 5s,6s,5p,6p,5d,2.6d,4f,-0.2f,G -r 
>> 2.40,3.15,2.70,3.15 -0 5,2.15 -sw -f PBE
>>    gpaw dataset Eu -P 5s,6s,5p,6p,5d,3.6d,4f,0.3f,G -r 
>> 3.15,3.10,3.05,2.85 -0 5,2.65 -sw -f PBE
>>    gpaw dataset Gd -P 5s,6s,5p,6p,5d,1.9d,4f,1.0f,G -r 
>> 2.95,2.55,2.50,2.65 -0 5,2.45 -sw -f PBE
>>    gpaw dataset Tb -P 5s,6s,5p,6p,5d,4.1d,4f,0.6f,G -r 
>> 2.45,2.95,2.80,2.65 -0 5,2.20 -sw -f PBE
>>    gpaw dataset Dy -P 5s,6s,5p,6p,5d,2.5d,4f,0.7f,G -r 
>> 2.70,3.35,2.90,3.10 -0 5,2.50 -sw -f PBE
>>    gpaw dataset Ho -P 5s,6s,5p,6p,5d,0.9d,4f,-0.3f,G -r 
>> 2.35,3.15,3.00,3.35 -0 5,2.25 -sw -f PBE
>>    gpaw dataset Er -P 5s,6s,5p,6p,5d,0.8d,4f,0.0f,G -r 
>> 2.75,2.85,2.55,3.00 -0 5,2.30 -sw -f PBE
>>    gpaw dataset Tm -P 5s,6s,5p,6p,5d,2.2d,4f,4.3f,G -r 
>> 2.70,2.90,3.20,2.65 -0 5,2.15 -sw -f PBE
>>    gpaw dataset Yb -P 5s,6s,5p,6p,5d,4.3d,4f,0.1f,G -r 
>> 2.80,3.00,2.60,2.80 -0 5,2.15 -sw -f PBE
>>    gpaw dataset Lu -P 5s,6s,5p,6p,5d,-1.1d,4f,-0.7f,G -r 
>> 2.65,2.70,2.75,2.55 -0 5,2.30 -sw -f PBE
>>
>> You need latest master or version 1.4.0 with this small change:
>>
>> https://gitlab.com/gpaw/gpaw/commit/34058482
>>
>> Jens Jørgen
>>
>>> Regards,
>>> Merrick
>>> On 05/30/2018 03:36 PM, shijm89 via gpaw-users wrote:
>>> > Hi
>>> > I'm interested in doing some calculations involving rare earth elements. 
>>>
>>> > I found there is no PAW setup for these element, so I tried generating 
>>>
>>> > setups by myself.
>>> > I tried
>>> > gpaw dataset La -f PBE -s -w
>>> > and
>>> > gpaw dataset Ce -f PBE -s -w
>>> > I did get setups file with no error.
>>> > But after I calculated the lattice constant of La and Ce, I found that 
>>>
>>> > the results are not so close to expremental data.
>>> > Is this because the setups are not valid?
>>> What experimental data did you compare to?
>>> > Or did I do somethings wrong?
>>> > How can I get some valid setups for REM?
>>> > I found a paper which gives PAW datasets for REMs, is it possible to
>>> > use them in GPAW?
>>> I don't think so.
>>> > Accurate projected augmented wave (PAW) datasets for rare-earth
>>> > elements (RE=La-Lu)
>>> > http://www.vlab.msi.umn.edu/resources/repaw/index.shtml
>>> That link does not work for me.  Here are some calculations for
>>> RE-nitrides you could compare to:
>>> http://dx.doi.org/10.1016/j.commatsci.2014.07.030
>>> I also have some experimental PAW datasets I could give you if you want. 
>>>
>>> Jens Jørgen
>>> > Regards,
>>> > Merrick
>>> >
>>> >
>>> > _______________________________________________
>>> > gpaw-users mailing list
>>> > gpaw-users at listserv.fysik.dtu.dk
>>> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>

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