Dear QE users,
Greetings! Last week I posted a problem related to vibration analysis
(https://www.mail-archive.com/[email protected]/msg37294.html),
unfortunately I didn’t get responses. In the past week I did several trials and
got some new results. But I still cannot completely figure out my confusions. I
would really appreciate it if some one could give me some advice and
instructions.
Basically my question is:
1) When doing frequency analysis for molecules, I expected to get zero or
extremely small value for the first six frequencies (i.e. translational &
rotational modes). According to suggestions from those previously posted
problems, I tried to apply more restrict convergence thresholds and ASR. It
seems that ASR help a lot to reduce the number. But I still got frequencies at
~50 level. Is it possible to completely remove those small values? Or are those
values small enough to be neglected?
Following are the I/O file of ph.x:
=======================================phonon
input=======================================
phonons of CH4
&inputph
tr2_ph=1.0d-16,
prefix='ch4_cell2',
amass(1)=12.011,
amass(2)=1.0,
alpha_mix(1)=0.1,
asr=.true.
outdir='./ts/tmp/',
fildyn='CH4_cell3.dynG'
/
0.0 0.0 0.0
The calculated frequencies are:
=======================================phonon
output=======================================
freq ( 1) = -0.507756 [THz] = -16.936932 [cm-1]
freq ( 2) = -0.459728 [THz] = -15.334860 [cm-1]
freq ( 3) = -0.271000 [THz] = -9.039597 [cm-1]
freq ( 4) = 1.535467 [THz] = 51.217660 [cm-1]
freq ( 5) = 1.705940 [THz] = 56.904033 [cm-1]
freq ( 6) = 1.741249 [THz] = 58.081818 [cm-1]
freq ( 7) = 38.593830 [THz] = 1287.351595 [cm-1]
freq ( 8) = 38.610060 [THz] = 1287.892987 [cm-1]
freq ( 9) = 38.618418 [THz] = 1288.171751 [cm-1]
freq ( 10) = 45.381162 [THz] = 1513.752629 [cm-1]
freq ( 11) = 45.388200 [THz] = 1513.987398 [cm-1]
freq ( 12) = 89.406470 [THz] = 2982.278836 [cm-1]
freq ( 13) = 92.546906 [THz] = 3087.032485 [cm-1]
freq ( 14) = 92.772395 [THz] = 3094.554013 [cm-1]
freq ( 15) = 92.773975 [THz] = 3094.606712 [cm-1]
2) My ultimate goal is to perform frequency analysis for adsorbate so that I
can both determine transition state structures and apply ZPE corrections. I
tried to use “nat_todo” to fix the surface atoms and only did calculation for
adsorbate (CH in my case). I got crazy result (~10000 cm-1) when using large
tr2_ph, and got improved results when I decrease the threshold. But I still got
fairly large translational & rotational frequencies like below:
freq ( 1) = -25.618746 [THz] = -854.549399 [cm-1]
freq ( 2) = -7.333895 [THz] = -244.632409 [cm-1]
freq ( 3) = -6.696884 [THz] = -223.383991 [cm-1]
freq ( 4) = -6.248674 [THz] = -208.433322 [cm-1]
freq ( 5) = -4.947831 [THz] = -165.041892 [cm-1]
freq ( 6) = -2.014699 [THz] = -67.203109 [cm-1]
freq ( 37) = 0.571458 [THz] = 19.061786 [cm-1]
freq ( 38) = 5.754719 [THz] = 191.956759 [cm-1]
freq ( 39) = 16.488930 [THz] = 550.011494 [cm-1]
freq ( 40) = 16.563150 [THz] = 552.487199 [cm-1]
freq ( 41) = 18.255969 [THz] = 608.953585 [cm-1]
freq ( 42) = 56.121326 [THz] = 1872.005923 [cm-1]
What does negative translational frequencies indicate, is it possible to
eliminate these imaginary numbers (like using more restrict threshold)?
And does my result indicate that my structure is most probably not a transition
state since all the other frequencies are positive?
I’m attaching the input file of pw.x &ph.x below:
=========================scf input, structure obtained from
neb.x========================
&CONTROL
Calculation='scf',
restart_mode='from_scratch',
prefix = "Ni_ch_ts"
outdir = "./ts/tmp",
pseudo_dir = "./pseudo",
tstress = .true.
verbosity = 'high'
tefield = .true.
dipfield = .true.
/
&SYSTEM
ibrav = 0,
nat = 14,
ntyp = 3,
ecutwfc = 65,
ecutrho = 650,
Occupations='smearing',
smearing='mp',
degauss=0.01,
nspin=2,
starting_magnetization(1)=0.2,
eamp = 0.0
edir = 3
emaxpos = 0.95
eopreg = 0.05
/
&ELECTRONS
electron_maxstep=250,
conv_thr = 1.D-10,
mixing_beta = 0.1,
/
ATOMIC_SPECIES
Ni 58.69 ni_pbe_v1.4.uspp.F.UPF
C 12 C.pbe-n-kjpaw_psl.1.0.0.UPF
H 1 H.pbe-kjpaw_psl.1.0.0.UPF
CELL_PARAMETERS { angstrom }
4.9667177200 0.0000000000 0.0000000000
2.4833588600 4.3013037190 0.0000000000
0.0000000000 0.0000000000 20.000000000
ATOMIC_POSITIONS { angstrom }
Ni 0.0000000000 0.0000000000 7.9723500000
Ni 1.2416800000 2.1506500000 7.9723500000
Ni 2.4833600000 0.0000000000 7.9723500000
Ni 3.7250400000 2.1506500000 7.9723500000
Ni 2.4833600000 1.4337700000 10.0000000000
Ni 3.7250400000 3.5844200000 10.0000000000
Ni 4.9667200000 1.4337700000 10.0000000000
Ni 6.2084000000 3.5844200000 10.0000000000
Ni 1.2281125212 0.7413038538 12.1124602290
Ni 2.4833613443 2.9495126082 12.0722664849
Ni 3.7386101535 0.7413040204 12.1124604793
Ni 4.9667205066 2.8946406480 11.9560276983
C 2.4833610952 1.4972020489 13.1166864267
H 2.4833559794 3.1940064219 13.5465576823
K_POINTS { automatic }
6 6 1 0 0 0
=======================================ph.x
input=======================================
phonons of CH on metal Ni at Gamma
&inputph
tr2_ph=1.0d-16,
prefix='Ni_ch_ts',
epsil=.false.,
amass(1)=58.69,
amass(2)=12.011,
amass(3)=1.0,
alpha_mix(1)=0.1,
outdir='./tmp/',
fildyn='CH.dynG',
nat_todo= 2,
/
0.0 0.0 0.0
13 14
Thanks in advance for anyone that could give suggestions to me!
Best regards
Ziheng Shen
PhD student @ Georgia Institute of Technology
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