[gpaw-users] about PAW datasets for rare earth elements
shijm89
shijm89 at 163.com
Tue Aug 21 14:07:12 CEST 2018
Thank you for help.
I'm confused, since I already tried the 1.4.1b1 version.
So you means that I should try the master version?
On 08/21/2018 05:49 AM, shijm89 wrote:
Thanks for the hint.
I have tried to insert the print statment, but I can not see anything from the output.
OK, I am now able to reproduce your result if I add "--create-basis-set" on the command line. Latest version of GPAW does not create a basis set unless you ask for it. So, if you use that version, you should be fine.
Jens Jørgen
here is the output before I insert the command.
Z: 59
Name: Praseodymium
Symbol: Pr
XC-functional: PBE
Equation: Schrödinger
Grid points: 2000 (0.00000, 0.00012, 0.00024, ..., 40.109, 43.777)
Exponents: 50 (0.010, 0.014, ..., 123852.612, 174050.000)
Basis functions: 38, 42, 45, 48 (s, p, d, f)
Solving non-relativistic Schrödinger equation using Gaussian basis-set:
.......................................................
Converged in 54 steps
state occupation eigenvalue <r>
nl [Hartree] [eV] [Bohr]
-----------------------------------------------------
1s 2.000 -1458.572075 -39689.76776 0.026
2s 2.000 -227.582496 -6192.83514 0.110
2p 6.000 -215.488117 -5863.73034 0.094
3s 2.000 -48.970155 -1332.54579 0.287
3p 6.000 -43.711528 -1189.45126 0.277
3d 10.000 -33.913516 -922.83377 0.248
4s 2.000 -9.607125 -261.42317 0.654
4p 6.000 -7.630834 -207.64556 0.674
4d 10.000 -4.157232 -113.12406 0.726
5s 2.000 -1.293333 -35.19338 1.590
5p 6.000 -0.775567 -21.10426 1.801
4f 3.000 -0.147318 -4.00872 1.089
6s 2.000 -0.120401 -3.27627 4.726
5d 0.000 -0.094003 -2.55794 3.144
6p 0.000 -0.049918 -1.35833 6.169
Energies: [Hartree] [eV]
--------------------------------------------
kinetic +8919.467260 +242711.06674
coulomb (e-e) +3508.273846 +95464.99390
coulomb (e-n) -21142.587202 -575319.10192
xc -208.432815 -5671.74579
total -8923.278912 -242814.78707
Exact exchange energy: -204.812787 Hartree, -5573.23981 eV
Solving scalar-relativistic Schrödinger equation using finite difference:
...................................................................
Converged in 66 steps
state occupation eigenvalue <r>
nl [Hartree] [eV] [Bohr]
-----------------------------------------------------
1s 2.000 -1536.748679 -41817.06152 0.024
2s 2.000 -247.225629 -6727.35203 0.103
2p 6.000 -221.200001 -6019.15861 0.091
3s 2.000 -53.337052 -1451.37510 0.272
3p 6.000 -45.095311 -1227.10591 0.270
3d 10.000 -33.529275 -912.37804 0.247
4s 2.000 -10.601806 -288.48985 0.622
4p 6.000 -7.909779 -215.23605 0.659
4d 10.000 -4.060953 -110.50417 0.727
5s 2.000 -1.434246 -39.02781 1.508
5p 6.000 -0.789152 -21.47392 1.767
6s 2.000 -0.127243 -3.46245 4.499
5d 0.000 -0.074375 -2.02385 3.327
4f 3.000 -0.045833 -1.24717 1.211
6p 0.000 -0.045766 -1.24537 6.181
Energies: [Hartree] [eV]
--------------------------------------------
kinetic +9810.823915 +266966.11677
coulomb (e-e) +3578.426750 +97373.95164
coulomb (e-n) -22410.790914 -609828.68267
xc -215.752743 -5870.93117
total -9237.292992 -251359.54542
Exact exchange energy: -211.934912 Hartree, -5767.04270 eV
Generating PAW PBE setup for Pr
Shape function: exp(-alpha*r^2), alpha=2.6 Bohr^-2
Core electrons: 46.0
Valence electrons: 13.0
Local potential matching g-scattering at e=0.0 eV and r=2.00 Bohr
Constructing smooth pseudo core density for r < 2.244
Pseudo core electrons: 0.212095
Projectors:
state occ energy norm rcut
nl [Hartree] [eV] [electrons] [Bohr]
----------------------------------------------------------
5s 2.00 -1.434246 -39.02781 0.637 2.95
6s 2.00 -0.127243 -3.46245 0.974 2.95
5p 6.00 -0.789152 -21.47392 0.762 2.65
6p 0.00 -0.045766 -1.24537 0.985 2.65
5d 0.00 -0.074375 -2.02385 0.984 2.30
d 2.200000 59.86505 2.30
4f 3.00 -0.045833 -1.24717 0.290 2.05
f 0.400000 10.88455 2.05
Checking eigenvalues of Pr pseudo atom using a Gaussian basis set:
AE [eV] PS [eV] error [eV]
1s 2 -41817.062
2s 2 -6727.352
3s 2 -1451.375
4s 2 -288.490
5s 2 -39.028 -39.021 0.007
6s 2 -3.462 -3.467 -0.005
-0.081 -0.081 0.000
0.875 0.853 -0.023
2.695 2.634 -0.061
5.951 5.825 -0.127
11.858 11.525 -0.333
22.800 21.866 -0.934
2p 6 -6019.159
3p 6 -1227.106
4p 6 -215.236
5p 6 -21.474 -21.455 0.019
6p 0 -1.245 -1.246 -0.001
0.263 0.289 0.026
1.150 1.180 0.030
2.857 2.883 0.026
5.680 5.710 0.029
10.305 10.323 0.018
18.006 18.004 -0.003
3d 10 -912.378
4d 10 -110.504
5d 0 -2.024 -2.017 0.007
0.300 0.352 0.052
0.880 0.950 0.070
2.065 2.163 0.098
3.932 4.071 0.139
6.827 6.993 0.166
11.356 11.550 0.195
4f 3 -1.247 -1.211 0.036
0.654 0.667 0.013
1.324 1.372 0.047
2.427 2.495 0.069
4.087 4.194 0.107
6.500 6.638 0.137
10.031 10.207 0.176
/home/loampc-b/GPAW/gpaw-1.3.1/gpaw/atom/aeatom.py:298: RuntimeWarning: invalid value encountered in double_scalars
ag = np.exp(-(-2 * e)**0.5 * (r_g[gmax - 2] - r_g[gmax - 1]))
and here is the output after I inserted print(e) before line:298.
Z: 59
Name: Praseodymium
Symbol: Pr
XC-functional: PBE
Equation: Schrödinger
Grid points: 2000 (0.00000, 0.00012, 0.00024, ..., 40.109, 43.777)
Exponents: 50 (0.010, 0.014, ..., 123852.612, 174050.000)
Basis functions: 38, 42, 45, 48 (s, p, d, f)
Solving non-relativistic Schrödinger equation using Gaussian basis-set:
.......................................................
Converged in 54 steps
state occupation eigenvalue <r>
nl [Hartree] [eV] [Bohr]
-----------------------------------------------------
1s 2.000 -1458.572075 -39689.76776 0.026
2s 2.000 -227.582496 -6192.83514 0.110
2p 6.000 -215.488117 -5863.73034 0.094
3s 2.000 -48.970155 -1332.54579 0.287
3p 6.000 -43.711528 -1189.45126 0.277
3d 10.000 -33.913516 -922.83377 0.248
4s 2.000 -9.607125 -261.42317 0.654
4p 6.000 -7.630834 -207.64556 0.674
4d 10.000 -4.157232 -113.12406 0.726
5s 2.000 -1.293333 -35.19338 1.590
5p 6.000 -0.775567 -21.10426 1.801
4f 3.000 -0.147318 -4.00872 1.089
6s 2.000 -0.120401 -3.27627 4.726
5d 0.000 -0.094003 -2.55794 3.144
6p 0.000 -0.049918 -1.35833 6.169
Energies: [Hartree] [eV]
--------------------------------------------
kinetic +8919.467260 +242711.06674
coulomb (e-e) +3508.273846 +95464.99390
coulomb (e-n) -21142.587202 -575319.10192
xc -208.432815 -5671.74579
total -8923.278912 -242814.78707
Exact exchange energy: -204.812787 Hartree, -5573.23981 eV
Solving scalar-relativistic Schrödinger equation using finite difference:
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.-1536.748857002552
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.
Converged in 66 steps
state occupation eigenvalue <r>
nl [Hartree] [eV] [Bohr]
-----------------------------------------------------
1s 2.000 -1536.748679 -41817.06152 0.024
2s 2.000 -247.225629 -6727.35203 0.103
2p 6.000 -221.200001 -6019.15861 0.091
3s 2.000 -53.337052 -1451.37510 0.272
3p 6.000 -45.095311 -1227.10591 0.270
3d 10.000 -33.529275 -912.37804 0.247
4s 2.000 -10.601806 -288.48985 0.622
4p 6.000 -7.909779 -215.23605 0.659
4d 10.000 -4.060953 -110.50417 0.727
5s 2.000 -1.434246 -39.02781 1.508
5p 6.000 -0.789152 -21.47392 1.767
6s 2.000 -0.127243 -3.46245 4.499
5d 0.000 -0.074375 -2.02385 3.327
4f 3.000 -0.045833 -1.24717 1.211
6p 0.000 -0.045766 -1.24537 6.181
Energies: [Hartree] [eV]
--------------------------------------------
kinetic +9810.823915 +266966.11677
coulomb (e-e) +3578.426750 +97373.95164
coulomb (e-n) -22410.790914 -609828.68267
xc -215.752743 -5870.93117
total -9237.292992 -251359.54542
Exact exchange energy: -211.934912 Hartree, -5767.04270 eV
Generating PAW PBE setup for Pr
Shape function: exp(-alpha*r^2), alpha=2.6 Bohr^-2
Core electrons: 46.0
Valence electrons: 13.0
Local potential matching g-scattering at e=0.0 eV and r=2.00 Bohr
Constructing smooth pseudo core density for r < 2.244
Pseudo core electrons: 0.212095
Projectors:
state occ energy norm rcut
nl [Hartree] [eV] [electrons] [Bohr]
----------------------------------------------------------
5s 2.00 -1.434246 -39.02781 0.637 2.95
6s 2.00 -0.127243 -3.46245 0.974 2.95
5p 6.00 -0.789152 -21.47392 0.762 2.65
6p 0.00 -0.045766 -1.24537 0.985 2.65
5d 0.00 -0.074375 -2.02385 0.984 2.30
d 2.200000 59.86505 2.30
4f 3.00 -0.045833 -1.24717 0.290 2.05
f 0.400000 10.88455 2.05
Checking eigenvalues of Pr pseudo atom using a Gaussian basis set:
AE [eV] PS [eV] error [eV]
1s 2 -41817.062
2s 2 -6727.352
3s 2 -1451.375
4s 2 -288.490
5s 2 -39.028 -39.021 0.007
6s 2 -3.462 -3.467 -0.005
-0.081 -0.081 0.000
0.875 0.853 -0.023
2.695 2.634 -0.061
5.951 5.825 -0.127
11.858 11.525 -0.333
22.800 21.866 -0.934
2p 6 -6019.159
3p 6 -1227.106
4p 6 -215.236
5p 6 -21.474 -21.455 0.019
6p 0 -1.245 -1.246 -0.001
0.263 0.289 0.026
1.150 1.180 0.030
2.857 2.883 0.026
5.680 5.710 0.029
10.305 10.323 0.018
18.006 18.004 -0.003
3d 10 -912.378
4d 10 -110.504
5d 0 -2.024 -2.017 0.007
0.300 0.352 0.052
0.880 0.950 0.070
2.065 2.163 0.098
3.932 4.071 0.139
6.827 6.993 0.166
11.356 11.550 0.195
4f 3 -1.247 -1.211 0.036
0.654 0.667 0.013
1.324 1.372 0.047
2.427 2.495 0.069
4.087 4.194 0.107
6.500 6.638 0.137
10.031 10.207 0.176
-1.4342456713610958
-1.4211415048330842
-1.42386441186401
-1.4240317106374174
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-0.12570883070209166
-0.12570968630991655
-0.7891521386923156
-0.775470603000201
-0.7770977782759291
-0.777100701704022
-0.045766333471354774
-0.03721537494121601
-0.03843444300495611
-0.03846766795386405
-0.07437520238237472
-0.06002324426095391
-0.06284684813753705
-0.0630688159943579
-0.06306925012833252
-0.04583277423137479
-0.04215890004529653
-0.038775455294252796
-0.011735372146105375
0.08497487873538354
/home/loampc-b/GPAW/gpaw-1.3.1/gpaw/atom/aeatom.py:298: RuntimeWarning: invalid value encountered in double_scalars
ag = np.exp(-(-2 * e)**0.5 * (r_g[gmax - 2] - r_g[gmax - 1]))
nan
nan
nan
nan
nan
nan
nan
...
following endless nan
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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