[ase-users] [ase-developers] Units in ASE
John Kitchin
jkitchin at andrew.cmu.edu
Wed Apr 3 14:51:58 CEST 2013
It looks like VASP uses different masses than ase.data. Here is a
comparison of what is in ase.data, vs POMASS in the POTCAR files. This
could be some part of your differences.
sym ase-mass vasp-mass delta
X 0.000000None None
H 1.007940 1.0 0.00794
He 4.002600 4.0 0.0026
Li 6.941000 7.01 -0.069
Be 9.012180 9.013 -0.000819999999999
B 10.811000 10.811 0.0
C 12.011000 12.011 0.0
N 14.006700 14.001 0.0057
O 15.999400 16.0 -0.0006
F 18.998400 18.998 0.000399999999999
Ne 20.179700 20.18 -0.000299999999999
Na 22.989770 22.99 -0.000229999999998
Mg 24.305000 24.305 0.0
Al 26.981540 26.982 -0.00046
Si 28.085500 28.085 0.000499999999999
P 30.973760 30.974 -0.000240000000002
S 32.066000 32.066 0.0
Cl 35.452700 35.453 -0.000300000000003
Ar 39.948000 39.949 -0.000999999999998
K 39.098300None None
Ca 40.078000 40.078 0.0
Sc 44.955900 44.956 -0.000100000000003
Ti 47.880000 47.88 0.0
V 50.941500 50.941 0.000499999999995
Cr 51.996000 51.996 0.0
Mn 54.938000 54.938 0.0
Fe 55.847000 55.847 0.0
Co 58.933200 58.933 0.0002
Ni 58.693400 58.69 0.0034
Cu 63.546000 63.546 0.0
Zn 65.390000 65.39 0.0
Ga 69.723000 69.723 0.0
Ge 72.610000 72.61 0.0
As 74.921600 74.922 -0.000399999999999
Se 78.960000 78.96 0.0
Br 79.904000 79.904 0.0
Kr 83.800000 83.8 0.0
Rb 85.467800None None
Sr 87.620000 87.62 0.0
Y 88.905900None None
Zr 91.224000 91.224 0.0
Nb 92.906400None None
Mo 95.940000 95.94 0.0
Tc nan 98.906 nan
Ru 101.070000 101.07 0.0
Rh 102.905500 102.906 -0.000500000000002
Pd 106.420000 106.42 0.0
Ag 107.868000 107.868 0.0
Cd 112.410000 112.411 -0.001
In 114.820000 114.82 0.0
Sn 118.710000 118.71 0.0
Sb 121.757000 121.75 0.00700000000001
Te 127.600000 127.6 0.0
I 126.904500 126.904 0.000500000000002
Xe 131.290000 131.294 -0.00400000000002
Cs 132.905400None None
Ba 137.330000None None
La 138.905500 138.9 0.00549999999998
Ce 140.120000 140.115 0.005
Pr 140.907700 140.907 0.000699999999995
Nd 144.240000 144.24 0.0
Pm nan 146.915 nan
Sm 150.360000 150.36 0.0
Eu 151.965000 151.965 0.0
Gd 157.250000 157.25 0.0
Tb 158.925300 158.925 0.000299999999982
Dy 162.500000 162.5 0.0
Ho 164.930300 164.93 0.000299999999982
Er 167.260000 167.26 0.0
Tm 168.934200 168.93 0.0042
Yb 173.040000 173.04 0.0
Lu 174.967000 174.967 0.0
Hf 178.490000 178.49 0.0
Ta 180.947900 180.948 -0.000100000000003
W 183.850000 183.85 0.0
Re 186.207000 186.207 0.0
Os 190.200000 190.2 0.0
Ir 192.220000 192.22 0.0
Pt 195.080000 195.08 0.0
Au 196.966500 196.966 0.000499999999988
Hg 200.590000 200.59 0.0
Tl 204.383000 204.38 0.00300000000001
Pb 207.200000 207.2 0.0
Bi 208.980400 208.98 0.000400000000013
Po nan 208.942 nan
At nan 209.987 nan
Rn nan 22.017 nan
Fr nanNone None
Ra 226.025400None None
Ac nan 227.028 nan
Th 232.038100 232.039 -0.000900000000001
Pa 231.035900 231.036 -0.000100000000003
U 238.029000 238.029 0.0
Np 237.048200 237.048 0.000200000000007
Pu nan 244.064 nan
Am nan 243.061 nan
Cm nanNone None
Bk nanNone None
Cf nanNone None
Es nanNone None
Fm nanNone None
Md nanNone None
No nanNone None
Lr nanNone None
John
-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu
On Tue, Apr 2, 2013 at 12:33 PM, Gaël Donval <gael.donval at cnrs-imn.fr>wrote:
> Dear all,
>
> I'm working on integrating VASP velocities in ASE.
>
> VASP always outputs velocities in A/fs (one can give velocities as
> base_vector/time_step but this is not the point here).
>
> I had problems recalculating the kinetic energy and the temperature from
> ASE using the appropriate functions: atoms.get_kinetic_energy() and
> atoms.get_temperature(). Here is what I did:
>
> 1) Convert units to SI (I'm more comfortable with them):
> mass_si = mass * ase.units._amu # Da to kg
> v_si = v_vasp * 1e5 # A/fs to m/s
>
> 2) Calculate the kinetic energy in eV:
> ((mass_si*(v_si**2).sum(axis=1)/2.)*units.J).sum() # in eV
>
> 3) Calculate the temperature in Kelvins:
> (2*ekin/(3*len(atoms)))/units.kB
>
> I could compare 2) and 3) with the results given in VASP. Basically, I
> get almost the same values, but not exactly (VASP: 5.326 eV,
> Calculations: 5.313 eV). I'm curious to get your opinion about this
> difference. I know the mass and the velocity with at least 6
> significative figures ... I acknowledge that these results are close
> from each other but I expect at the very least 4 identical figures here.
> Maybe the masses...
>
>
> This is not all. When I use ase and put the velocities in as m/s, just
> like above, the calculated energies and temperatures are completely off
> (by a factor of 100, Ek=0.05434 u. --this is not even 0.05313...).
>
> I guessed this was because of units. I can't change masses, but only
> velocities. Since I have a factor of around 100, I just had to multiply
> my velocities by 10. The problem is that I don't see how that would make
> sensible units. Would anyone more familiar with atomic sets of units be
> willing to shed light on this?
>
> Thanks in advance,
> Gael
>
>
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