Vibrational frequencies of CO on Ni 111 surface: Difference between revisions
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{{Sur_sci - Tutorial}} | |||
== Task == | |||
Calculation of the vibrational frequencies of CO@Ni(111) (on top). | |||
== Input == | |||
=== {{TAG|POSCAR}} === | |||
<pre> | <pre> | ||
Ni - (111) + CO | Ni - (111) + CO on-top | ||
3.53000000000000 | 3.53000000000000 | ||
0.7071067800000000 0.0000000000000000 0.0000000000000000 | 0.7071067800000000 0.0000000000000000 0.0000000000000000 | ||
-0.3535533900000000 0.6123724000000000 0.0000000000000000 | -0.3535533900000000 0.6123724000000000 0.0000000000000000 | ||
0.0000000000000000 0.0000000000000000 5. | 0.0000000000000000 0.0000000000000000 5.1961523999999999 | ||
5 | Ni C O | ||
5 1 1 | |||
Selective dynamics | Selective dynamics | ||
Direct | Direct | ||
Line 41: | Line 21: | ||
0.3333333300000021 0.6666666699999979 0.1111111100000031 F F F | 0.3333333300000021 0.6666666699999979 0.1111111100000031 F F F | ||
0.6666666699999979 0.3333333300000021 0.2222222199999990 F F F | 0.6666666699999979 0.3333333300000021 0.2222222199999990 F F F | ||
-0.0000000000000000 0.0000000000000000 0.3326227833039623 F F F | |||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.4445699380869117 F F F | ||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.5403264650180125 F F T | ||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.6032949698060487 F F T | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
Line 55: | Line 35: | ||
</pre> | </pre> | ||
Try to change the selective dynamics tag such that displacements | *Frequencies only for the CO molecule and the z-direction (z- and (x,y) are independent). | ||
N.B.: this {{FILE|POSCAR}} is essentially the result ({{FILE|CONTCAR}} file) of the relaxation performed in the [[CO on Ni 111 surface]] example. | |||
=== {{TAG|INCAR}} === | |||
{{TAGBL|SYSTEM}} = CO on Ni111 - frequencies | |||
general: | |||
{{TAGBL|ENMAX}} = 400 | |||
{{TAGBL|ISMEAR}} = 2 ; {{TAGBL|SIGMA}} = 0.2 | |||
{{TAGBL|ALGO}} = Fast | |||
{{TAGBL|EDIFF}} = 1E-6 | |||
{{TAGBL|MAXMIX}} = 60 # reuse the mixer between ionic steps, saves time | |||
dynamic: | |||
{{TAGBL|NSW}} = 100 | |||
{{TAGBL|IBRION}} = 5 | |||
{{TAGBL|NFREE}} = 2 | |||
*Small termination criterion ({{TAG|EDIFF}}). | |||
*Automatic frequency calculation (displacement 0.04 <math>\AA</math>). | |||
*Reuse of the mixer between ionic steps ({{TAG|MAXMIX}}) to save time. | |||
=== {{TAG|KPOINTS}} === | |||
<pre> | |||
k-points | |||
0 | |||
Monkhorst-Pack | |||
9 9 1 | |||
0 0 0 | |||
</pre> | |||
== Calculation == | |||
*Finite differences give the following additional output in the {{TAG|OUTCAR}} fiel for frequency calculations: | |||
Finite differences progress: | |||
Degree of freedom: 1/ 2 | |||
Displacement: 1/ 2 | |||
Total: 1/ 4 | |||
*After the first calculation for the equilibrium geometry, {{TAG|NFREE}} displacements (<math>\pm</math>{{TAG|POTIM}}) are performed for each degree of freedom. From these displacements the dynamical matrix is set up and diagonalized. | |||
*At the end of the {{TAG|OUTCAR}} file the following are listed: | |||
**Forces. | |||
**The dynamical matrix and finally. | |||
**The eigenfrequencies. | |||
**Eigenvectors (first normalized and then mass-weighted). | |||
*The example output for the eigenvectors and eigenvalues of the dynamical matrix from the {{TAG|OUTCAR}} file should look like the following: | |||
Eigenvectors and eigenvalues of the dynamical matrix | |||
---------------------------------------------------- | |||
1 f = 63.914144 THz 401.584411 2PiTHz 2131.946301 cm-1 264.327748 meV | |||
X Y Z dx dy dz | |||
0.000000 0.000000 0.000000 0 0 0 | |||
0.000000 1.441116 2.038046 0 0 0 | |||
1.248043 0.720558 4.076093 0 0 0 | |||
0.000000 0.000000 6.108743 0 0 0 | |||
0.000000 1.441116 8.153979 0 0 0 | |||
0.000000 1.441116 9.908620 0 0 -0.761748 | |||
0.000000 1.441116 11.063296 0 0 0.623594 | |||
2 f = 12.467410 THz 78.335050 2PiTHz 415.868035 cm-1 51.561083 meV | |||
X Y Z dx dy dz | |||
0.000000 0.000000 0.000000 0 0 0 | |||
0.000000 1.441116 2.038046 0 0 0 | |||
1.248043 0.720558 4.076093 0 0 0 | |||
0.000000 0.000000 6.108743 0 0 0 | |||
0.000000 1.441116 8.153979 0 0 0 | |||
0.000000 1.441116 9.908620 0 0 -0.623594 | |||
0.000000 1.441116 11.063296 0 0 -0.781748 | |||
As one can see the first vibrational mode is the so-called ''CO stretch'' mode (stretching and contracting the C-O bond), | |||
whereas the second mode shows the CO molecule moving w.r.t. to the metallic surface (''CO-metal''). | |||
*Try to change the selective dynamics tag such that displacements | |||
in x and y direction are allowed as well for CO (note that | in x and y direction are allowed as well for CO (note that | ||
the selective dynamics flags always refer to cartesian coordinates), | the selective dynamics flags always refer to cartesian coordinates), | ||
i.e, | i.e, | ||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.5403264650180125 F F T | ||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.6032949698060487 F F T | ||
to | to | ||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.5403264650180125 T T T | ||
0.3333333300000021 0.6666666699999979 0. | 0.3333333300000021 0.6666666699999979 0.6032949698060487 T T T | ||
Also test whether you need to decrease {{TAG|EDIFF}} to 1E-8. | |||
== Download == | == Download == | ||
[ | [[Media:COonNi111_freq.tgz| COonNi111_freq.tgz]] | ||
{{Sur_sci}} | |||
[[Category:Examples]] | [[Category:Examples]] |
Latest revision as of 14:20, 14 November 2019
Overview > Ni 100 surface relaxation > Ni 100 surface DOS > Ni 100 surface bandstructure > Ni 111 surface relaxation > CO on Ni 111 surface > Ni 111 surface high precision > partial DOS of CO on Ni 111 surface > vibrational frequencies of CO on Ni 111 surface > STM of graphite > STM of graphene > collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation > List of tutorials
Task
Calculation of the vibrational frequencies of CO@Ni(111) (on top).
Input
POSCAR
Ni - (111) + CO on-top 3.53000000000000 0.7071067800000000 0.0000000000000000 0.0000000000000000 -0.3535533900000000 0.6123724000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 5.1961523999999999 Ni C O 5 1 1 Selective dynamics Direct 0.0000000000000000 0.0000000000000000 0.0000000000000000 F F F 0.3333333300000021 0.6666666699999979 0.1111111100000031 F F F 0.6666666699999979 0.3333333300000021 0.2222222199999990 F F F -0.0000000000000000 0.0000000000000000 0.3326227833039623 F F F 0.3333333300000021 0.6666666699999979 0.4445699380869117 F F F 0.3333333300000021 0.6666666699999979 0.5403264650180125 F F T 0.3333333300000021 0.6666666699999979 0.6032949698060487 F F T 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
- Frequencies only for the CO molecule and the z-direction (z- and (x,y) are independent).
N.B.: this POSCAR is essentially the result (CONTCAR file) of the relaxation performed in the CO on Ni 111 surface example.
INCAR
SYSTEM = CO on Ni111 - frequencies general: ENMAX = 400 ISMEAR = 2 ; SIGMA = 0.2 ALGO = Fast EDIFF = 1E-6 MAXMIX = 60 # reuse the mixer between ionic steps, saves time dynamic: NSW = 100 IBRION = 5 NFREE = 2
- Small termination criterion (EDIFF).
- Automatic frequency calculation (displacement 0.04 ).
- Reuse of the mixer between ionic steps (MAXMIX) to save time.
KPOINTS
k-points 0 Monkhorst-Pack 9 9 1 0 0 0
Calculation
- Finite differences give the following additional output in the OUTCAR fiel for frequency calculations:
Finite differences progress: Degree of freedom: 1/ 2 Displacement: 1/ 2 Total: 1/ 4
- After the first calculation for the equilibrium geometry, NFREE displacements (POTIM) are performed for each degree of freedom. From these displacements the dynamical matrix is set up and diagonalized.
- At the end of the OUTCAR file the following are listed:
- Forces.
- The dynamical matrix and finally.
- The eigenfrequencies.
- Eigenvectors (first normalized and then mass-weighted).
- The example output for the eigenvectors and eigenvalues of the dynamical matrix from the OUTCAR file should look like the following:
Eigenvectors and eigenvalues of the dynamical matrix ---------------------------------------------------- 1 f = 63.914144 THz 401.584411 2PiTHz 2131.946301 cm-1 264.327748 meV X Y Z dx dy dz 0.000000 0.000000 0.000000 0 0 0 0.000000 1.441116 2.038046 0 0 0 1.248043 0.720558 4.076093 0 0 0 0.000000 0.000000 6.108743 0 0 0 0.000000 1.441116 8.153979 0 0 0 0.000000 1.441116 9.908620 0 0 -0.761748 0.000000 1.441116 11.063296 0 0 0.623594 2 f = 12.467410 THz 78.335050 2PiTHz 415.868035 cm-1 51.561083 meV X Y Z dx dy dz 0.000000 0.000000 0.000000 0 0 0 0.000000 1.441116 2.038046 0 0 0 1.248043 0.720558 4.076093 0 0 0 0.000000 0.000000 6.108743 0 0 0 0.000000 1.441116 8.153979 0 0 0 0.000000 1.441116 9.908620 0 0 -0.623594 0.000000 1.441116 11.063296 0 0 -0.781748
As one can see the first vibrational mode is the so-called CO stretch mode (stretching and contracting the C-O bond), whereas the second mode shows the CO molecule moving w.r.t. to the metallic surface (CO-metal).
- Try to change the selective dynamics tag such that displacements
in x and y direction are allowed as well for CO (note that the selective dynamics flags always refer to cartesian coordinates), i.e,
0.3333333300000021 0.6666666699999979 0.5403264650180125 F F T 0.3333333300000021 0.6666666699999979 0.6032949698060487 F F T
to
0.3333333300000021 0.6666666699999979 0.5403264650180125 T T T 0.3333333300000021 0.6666666699999979 0.6032949698060487 T T T
Also test whether you need to decrease EDIFF to 1E-8.
Download
Overview > Ni 100 surface relaxation > Ni 100 surface DOS > Ni 100 surface bandstructure > Ni 111 surface relaxation > CO on Ni 111 surface > Ni 111 surface high precision > partial DOS of CO on Ni 111 surface > vibrational frequencies of CO on Ni 111 surface > STM of graphite > STM of graphene > collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation > List of tutorials