[ase-users] [ase-developers] Units in ASE
John Kitchin
jkitchin at andrew.cmu.edu
Thu Apr 4 02:50:21 CEST 2013
I would dig around in the source codes (of ase and Vasp) and see what each
one is doing.
j
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 Wed, Apr 3, 2013 at 11:16 AM, Gaël Donval <gael.donval at cnrs-imn.fr>wrote:
> I've seen that. I changed masses in ASE and I don't get better
> agreement: 5.358 eV (new calc) vs. 5.326 eV (VASP).
>
> Kinetic energies calculated using ASE are still off.
>
> Le mercredi 03 avril 2013 à 08:51 -0400, John Kitchin a écrit :
> > 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
> > >
> > >
> > > _______________________________________________
> > > ase-developers mailing list
> > > ase-developers at listserv.fysik.dtu.dk
> > > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-developers
> > >
> > 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
> >
> >
> > _______________________________________________
> > ase-developers mailing list
> > ase-developers at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-developers
> >
>
>
>
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