Question 1
I want to calculate the zero point energy for my system in order to compare my theoretical results with experimental data.Firstly, I have performed the geometry optimization calculations for my system. And secondly, I want to calculate the normal mode of my system. I wonder if my INCAR listed below is right, and if this kind of calculation will change my geometry again.
Thanks a lot!
Start parameter for this Run:
ISTART = 0
ICHARG = 2
INIWAV = 1
Electronic Relaxation:
ENCUT = 350
ENAUG = 550
PREC = Accurate
IALGO = 38
NELM = 60
NELMIN = 4
NELMDL = -5
EDIFF = 1E-05
NBANDS = 256
GGA = 91
VOSKOWN = 1
Ionic Relaxation:
EDIFFG = 1E-04
NSW = 1 ------> Do NSW=1 and ISIF =2 make me optimize the geometry again?
IBRION = 5
ISIF = 2
NFREE = 2
DOS related values:
SIGMA = 0.1
ISMEAR = 1
Spin polarized:
ISPIN = 2
no, if IBRION=5, no further geometry optimisation step is taken, the displacements of the atoms are just to determine the Hessian matrix.
Please do not forget to set POTIM to a small value which ensures that the displacements are in the harmonic regime
Question 2:
Hello Everyone,
I am wondering how to calculate the zero point energy ? Or is it included in the total energy EO in the OUTCAR file ?
Thank you
For a periodic system you need to calculate the phonon density of states. See the discussion here:
http://cms.mpi.univie.ac.at/vasp-forum/forum_viewtopic.php?4.1543
For an isolated molecule you need to do the vibrational analysis, just like any other quantum chemistry approach.
Qustion 3:
I would like to produce a phonon dispersion relation.
Can someone give me some hints where to start how to
proceed from the VASP generated output.
So far I have understood following:
1. IBRION=5 in INCAR is needed, together with ISYM =0
POTIM=0.03 (for example) and NSW=1.
2. For accurate results I need a large supercell and many k-points,
although I don't yet really understand why.
3. A third party software, called "PHONON", seems to produce a
phonon dispersion relation with VASP, although this was with older
versions of VASP. Can VASP version 4.6 do this without extra software?
Thank you,
Rob.
You need a large supercell because the "direct method" can only resolve phonons of a wavelength that fit inside the supercell. These wavelengths of course vary a lot with the material. For the crystals I deal with (complex metal hydrides) cells of edge length of the order of 10 Ang are sufficiently large.
You need accurate forces. I'm not convinced that you necessarily need many k-points, but then I usually converge my energies w.r.t. cutoff and k-points to sub-meV levels.
IBRION=5 will allow you to calculate phonons at the gamma point only. There are standard integrals to go from these to the dispersion relations. (See, for example, Maradudin et al., "Theory of lattice dynamics in the harmonic approximation" in Solid State Physics Supplement 3, Academic Press, New York, 1971.)
Phonon, available (at a price) either as part of the Materials Design suite or directly as a binary from Krzysztof Parlinski (http://wolf.ifj.edu.pl/phonon/), does the full k-space integration for accurate properties.
About the requirement of a large supercell, what I understand is that large supercells better reproduce the interactions(particularly long range) than their smaller counterparts. I do not understand how it is related to wavelength of phonon without much elaboration possibly with some refs.
You could try Parlinski, Li and Kawazoe, PRL 78 (1997) 4063. Though in my opinion it's not expressed very well there. The Phonon manual is better.
The phonons are only accurate for all wavevectors within your zone if the interactions with regions outside your supercell are negligible.
Thank you 'tjf' and 'bandy' for your comments.
I still have some basic questions:
1) When I use in my INCAR file
NSW=1
IBRION=5
POTIM=0.05
NFREE=2
ISYM=0
then is the corresponding output only in the OUTCAR file,
or is there more elsewhere?
2) I don't fully understand the related output in OUTCAR, neither
is it explained in the VASP guide. The relevant parts of the OUTCAR,
which I mostly do not understand, I have put here:
http://surfion.snu.ac.kr/~lahaye/vasp/
Also the corresponding INCAR and POSCAR files are there.
For example, what do the numbers in the DYNMAT header mean:
DYNMAT
------
1323
12.011
110.05000.00000.
0000
which corresponds to
?number-of-atoms?
mass-of-C-atom
??POTIM??
Thanks,
Rob.
the output lines are
DYNMAT
------
number of atom types (1) , number of atoms (of each type) (32), number of degrees of freedom (3)
atomic mass (es for each type)
#of the degree of freedom (1), #of the displacement (1) , displacement stepwidth (x,y,z) (POTIM 0.0 0.0)
admin wrote: ...
the output lines are
DYNMAT
------
number of atom types (1) , number of atoms (of each type) (32), number of degrees of freedom (3)
atomic mass (es for each type)
#of the degree of freedom (1), #of the displacement (1) , displacement stepwidth (x,y,z) (POTIM 0.0 0.0)
and the rest of the lines? They differ from the TOTAL-FORCES given in the OUTCAR file...
Question 4:
Finally "try and error" i found the rigt SMASS>0 value for my bulk system. now temperature ossilations behave nicely around the specified tempereture. For those who have trouble with crazy temperature ossilations in Nose-Hover, i recommend to try SMASS values on a small system with less accuracy until you get the ONE.
However at initial few steps temperature gets too high because of the un-corrected zero point energy, later it gets right if you have right SMASS value.
my question is:
do i need to do zero point energy corrections before i start a NTV kind MD.
thanks for any comments.
There is no zero point energy correction in classical dynamics. By definition, you are treating the nuclei classically.
Also, zero point energy is unrelated to the thermostat. An initial increase in temperature could be due to an unrelaxed initial geometry, but it could not have anything to do with zero point energy
Question 5
Author / Postminyork / Wed Oct 24 2007, 06:31PM /
Registered Member #862
Joined Sun Sep 10 2006, 01:27AM
posts 11 / Hi everyone,
I am trying to find out zero point energy.
I calculated vibrational frequencies.
The output looks like:
1 f = 8.061567 THz 50.652321 2PiTHz 268.904932 cm-1 33.339974 meV
/ Y Z dx dy dz
8.977990 6.624706 10.936994 0.006719 0.039428 -0.010154
7.987944 9.674310 9.806018 0.413037 -0.343292 0.197267
9.392611 10.883302 6.807745 -0.085214 -0.018862 0.038322
9.508228 8.622771 5.958509 -0.029949 0.024147 0.006505
8.899424 8.839951 11.853902 -0.042197 0.038273 -0.090672
6.120948 11.197274 9.536179 -0.366692 0.283409 0.284564
7.133821 10.473994 7.537471 0.239226 -0.169573 -0.496675
11.121763 9.271581 11.061170 -0.036620 -0.013825 -0.012190
10.227230 10.075736 8.974636 -0.059553 -0.004650 -0.004309
8.100989 7.451218 8.851565 -0.007203 0.058854 -0.000876
7.236704 8.224175 6.683469 -0.001378 0.084491 0.042668
11.212837 7.045694 10.155996 -0.010302 0.007806 0.001784
10.325511 7.861288 8.082347 -0.020102 0.014122 0.043694
2 f = 7.079362 THz 44.480941 2PiTHz 236.142080 cm-1 29.277897 meV
X Y Z dx dy dz
:
:
:
36 f = 0.013755 THz 0.086428 2PiTHz 0.458831 cm-1 0.056888 meV
X Y Z dx dy dz
8.977990 6.624706 10.936994 0.102093 0.019245 0.257813
7.987944 9.674310 9.806018 0.132338 0.029261 0.255157
9.392611 10.883302 6.807745 0.118728 -0.000978 0.240235
9.508228 8.622771 5.958509 0.078889 -0.005243 0.247438
8.899424 8.839951 11.853902 0.139986 0.023439 0.249408
6.120948 11.197274 9.536179 0.154355 0.057985 0.268958
7.133821 10.473994 7.537471 0.119275 0.034302 0.260041
11.121763 9.271581 11.061170 0.139385 -0.010396 0.228982
10.227230 10.075736 8.974636 0.130896 -0.005854 0.233723
8.100989 7.451218 8.851565 0.093099 0.023918 0.263760
7.236704 8.224175 6.683469 0.080405 0.029705 0.270179
11.212837 7.045694 10.155996 0.100642 -0.014724 0.235704
10.325511 7.861288 8.082347 0.091520 -0.010373 0.240363
37 f/i= 0.093217 THz 0.585702 2PiTHz 3.109395 cm-1 0.385516 meV
X Y Z dx dy dz
8.977990 6.624706 10.936994 0.239070 0.236352 0.052702
7.987944 9.674310 9.806018 0.199454 0.185082 -0.057749
9.392611 10.883302 6.807745 0.002953 -0.014170 -0.230647
9.508228 8.622771 5.958509 -0.092383 -0.066102 -0.103163
8.899424 8.839951 11.853902 0.331460 0.292073 -0.073353
6.120948 11.197274 9.536179 0.224907 0.223340 -0.011287
7.133821 10.473994 7.537471 0.049036 0.063376 -0.042926
11.121763 9.271581 11.061170 0.280827 0.218279 -0.256222
10.227230 10.075736 8.974636 0.144356 0.105320 -0.241512
8.100989 7.451218 8.851565 0.099915 0.125942 0.067740
7.236704 8.224175 6.683469 -0.046332 0.010972 0.084225
11.212837 7.045694 10.155996 0.189272 0.163435 -0.131329
10.325511 7.861288 8.082347 0.050095 0.050198 -0.115962
38 f/i= 0.154760 THz 0.972383 2PiTHz 5.162226 cm-1 0.640035 meV
X Y Z dx dy dz
8.977990 6.624706 10.936994 0.126384 -0.262807 -0.227082
7.987944 9.674310 9.806018 0.139611 -0.145411 0.066515
9.392611 10.883302 6.807745 0.006437 0.053658 0.085192
9.508228 8.622771 5.958509 -0.097969 0.116278 -0.098196
8.899424 8.839951 11.853902 0.232699 -0.333090 -0.049253
6.120948 11.197274 9.536179 0.172332 -0.064649 0.286356
7.133821 10.473994 7.537471 0.035081 0.054700 0.174680
11.121763 9.271581 11.061170 0.199668 -0.327237 -0.136729
10.227230 10.075736 8.974636 0.103914 -0.137326 -0.023564
8.100989 7.451218 8.851565 0.030719 -0.074162 -0.112721
7.236704 8.224175 6.683469 -0.068142 0.117870 -0.003848
11.212837 7.045694 10.155996 0.093973 -0.259108 -0.319251
10.325511 7.861288 8.082347 -0.001108 -0.069287 -0.202501
39 f/i= 0.244434 THz 1.535822 2PiTHz 8.153429 cm-1 1.010897 meV
X Y Z dx dy dz
8.977990 6.624706 10.936994 -0.357612 0.051833 0.052647
7.987944 9.674310 9.806018 0.040454 0.150719 -0.026591
9.392611 10.883302 6.807745 0.198217 -0.104919 -0.051938
9.508228 8.622771 5.958509 -0.083284 -0.138854 0.004243
8.899424 8.839951 11.853902 -0.072993 0.084775 -0.003256
6.120948 11.197274 9.536179 0.266850 0.419165 -0.067420
7.133821 10.473994 7.537471 0.144028 0.197717 -0.049322
11.121763 9.271581 11.061170 -0.015325 -0.222980 -0.008401
10.227230 10.075736 8.974636 0.092003 -0.157478 -0.030183
8.100989 7.451218 8.851565 -0.243674 0.111497 0.029157
7.236704 8.224175 6.683469 -0.136336 0.163984 0.006120
11.212837 7.045694 10.155996 -0.301781 -0.259147 0.048161
10.325511 7.861288 8.082347 -0.188592 -0.192250 0.025822
Questions:
1. how to distintiguish rotational and translational from vibrational ones?
Are they the ones with smallest frequencies?
2. In OUTCAR , there are two sets of frequencies:
One set is below:
Eigenvectors and eigenvalues of the dynamical matrix
------
the 2nd set is below:
Eigenvectors after division by SQRT(mass)
Eigenvectors and eigenvalues of the dynamical matrix
What is the difference and which one shall we use?
3.
What is the difference between
f= ....
and
f/i = ....
shown as below:
36 f = 0.013755 THz 0.086428 2PiTHz 0.458831 cm-1 0.056888 meV
X Y Z dx dy dz
8.977990 6.624706 10.936994 0.102093 0.019245 0.257813
7.987944 9.674310 9.806018 0.132338 0.029261 0.255157
9.392611 10.883302 6.807745 0.118728 -0.000978 0.240235
9.508228 8.622771 5.958509 0.078889 -0.005243 0.247438
8.899424 8.839951 11.853902 0.139986 0.023439 0.249408
6.120948 11.197274 9.536179 0.154355 0.057985 0.268958
7.133821 10.473994 7.537471 0.119275 0.034302 0.260041
11.121763 9.271581 11.061170 0.139385 -0.010396 0.228982
10.227230 10.075736 8.974636 0.130896 -0.005854 0.233723
8.100989 7.451218 8.851565 0.093099 0.023918 0.263760
7.236704 8.224175 6.683469 0.080405 0.029705 0.270179
11.212837 7.045694 10.155996 0.100642 -0.014724 0.235704
10.325511 7.861288 8.082347 0.091520 -0.010373 0.240363
37 f/i= 0.093217 THz 0.585702 2PiTHz 3.109395 cm-1 0.385516 meV
X Y Z dx dy dz
8.977990 6.624706 10.936994 0.239070 0.236352 0.052702
7.987944 9.674310 9.806018 0.199454 0.185082 -0.057749
Thanks,
Back to top /
admin / Thu Oct 25 2007, 10:28AM /
posts 1833 / 1) please look at the corresponding eigenvectors of the respective modes to find out the character.
2) the f/i are imaginary frequencies (either due to a translational shift of the unit cell or the complete molecule, or due to the softening of a mode due to phase transition or at a transition state)
Back to top /
minyork / Fri Oct 26 2007, 08:29PM /
Registered Member #862
Joined: Sun Sep 10 2006, 01:27AM
posts 11 / Thanks,
There is another problem:
The default value for POTIM is 0.015A.
How to decide the choice of POTIM is proper for a system?
For example, what will the proper choice of POTIM for
transition metals.
Back to top /
tsemi / Mon Feb 08 2010, 08:20PM /
Registered Member #2854
Joined: Mon Mar 09 2009, 02:38PM
Location: Golden Colorado USA
posts 16 / Hello,
When calculation vibrational frequencies, I get an output similar to the above posted one.
It seems that the vibrational frequency of each atom is listed. How does one extract the vibrational frequency of the system?
Thank you
Back to top /
forsdan / Mon Feb 08 2010, 08:30PM /
Registered Member #647
Joined: Mon Apr 24 2006, 11:07AM
Location: Gothenburg, Sweden
posts 280 / The vibrational frequencies given are the phonon modes at the gamma point. These modes are collective and are not for the individual atoms. Just look at the eigenvectors to confirm this.
What do you mean by that you want to extract the vibration frequency of the system? The frequencies are already given. If you want the zero-point energy just sum up the different energy contribution from all modes. Please elaborate on what you're after.
Best regards,
/Dan
Question 6:
Author / Postagainsmile / Sat Apr 21 2007, 04:08AM /
Registered Member #202
Joined Tue Jun 14 2005, 04:15PM
posts 6 / Hi all,
I'm a new user of VASP.
These days, I try to calculate zero point energy of H2 molecule.
I made an INCAR file as followings,
SYSTEM = H2
ISMEAR = 0
SIGMA = 0.01
ISIF = 1
ISPIN = 2
PREC = Accurate
NSW = 5
IBRION = 5
ENCUT = 875
VOSKOWN =1
NFREE = 2
POTIM = 0.02
IALGO =48
GGA = PE
EDIFF = 1E-5
Is there any problem in this? And where I can find the zero-point energy?
Thanks,
Back to top /
lcyin / Mon Apr 23 2007, 01:48PM /
Registered Member #109
Joined: Fri Mar 18 2005, 08:07AM
posts 30 / Seemly, your INCAR settings are right, and you can find the ZPE in the OUTCAR file, which looks like this:
1 f = 130.237331 THz 818.305288 2PiTHz 4344.249631 cm-1 538.618501 meV
Back to top /
admin / Wed May 02 2007, 02:07PM /
posts 1833 / please note that H is treated as a classical particle by VASP, though it is so light that it should be treated as a quantum particle.
[ Edited Wed May 02 2007, 02:08PM ]
[ Edited Wed May 02 2007, 02:09PM ]
Question 7: