STATE_new_tutorial/Cu110-CO_en - 第一原理分子動力学プログラム STATE Senri Wiki

CO/Cu(110)Interface †

CO/Cu(110)Interface

Introduction †

In this document, how to perform the vibrational analysis of atoms and molecules adsorbed on a surface using the finite difference (frozen phonon) method, by taking CO adsorbed on Cu(110). Here, in addition to the adsorbed CO molecule, the Cu atom underneath is also taken into account. The system is modeled using a 4-layer Cu(110) slab. Below is the input file of a CO adsorbed Cu(110) surface, which is already optimized. CO molecule and Cu atoms in the first and second layers of the slab was optimized.

↑

Input file †

nfinp.data

WF_OPT       DAV
NTYP         3
NATM         32
GMAX         6.00
GMAXP        20.00
KPOINT_MESH  4   4   1
KPOINT_SHIFT 1   1   0
NSTEP        200
MIX_ALPHA    0.30
SMEARING     MP
WIDTH        0.010
EDELTA       1.D-10
NEG          196
XCTYPE       vdW-DF2
ESM_BC       BC1
CPUMAX       1600.0
&CELL
     15.098909039006      0.000000000000      0.000000000000
      0.000000000000     14.235387960000      0.000000000000
      0.000000000000      0.000000000000     50.329696796687
&END
&ATOMIC_SPECIES
 Cu  63.54000 pot.Cu_pbe1
 C   12.01115 pot.C_pbe1
 O   15.99940 pot.O_pbe1
&END
&ATOMIC_COORDINATES CARTESIAN
      0.000003823996     -0.000001138123      3.702323615193    1    1    2
      0.000010283052     -0.000006912305      5.897216927318    1    1    3
      0.000000351042     -0.000002382316      0.053467056659    1    1    1
      5.089242487895     -0.000001108633     -0.208242367820    1    1    1
     10.009661676277      0.000001103467     -0.208241073609    1    1    1
      0.000001196465      7.117696353327     -0.191027901816    1    1    1
      5.012492707154      7.117697566474     -0.167155951780    1    1    1
     10.086413584750      7.117696561458     -0.167155627900    1    1    1
      2.507494428154      3.538363991660     -2.421985716480    1    1    1
      7.549453707970      3.590875576905     -2.405963340815    1    1    1
     12.591415007976      3.538365483794     -2.421988185457    1    1    1
      2.507492583039     10.697023879015     -2.421990853447    1    1    1
      7.549453621923     10.644515276442     -2.405964405967    1    1    1
     12.591413959874     10.697024958358     -2.421982246650    1    1    1
      0.000000000000      0.000000000000     -5.032969700311    1    0    1
      5.032969700311      0.000000000000     -5.032969700311    1    0    1
     10.065939338757      0.000000000000     -5.032969700311    1    0    1
      0.000000000000      7.117693980003     -5.032969700311    1    0    1
      5.032969700311      7.117693980003     -5.032969700311    1    0    1
     10.065939338757      7.117693980003     -5.032969700311    1    0    1
      2.516484819239      3.558846990002     -7.549454519543    1    0    1
      7.549454519543      3.558846990002     -7.549454519543    1    0    1
     12.582424219851      3.558846990002     -7.549454519543    1    0    1
      2.516484819239     10.676540969990     -7.549454519543    1    0    1
      7.549454519543     10.676540969990     -7.549454519543    1    0    1
     12.582424219851     10.676540969990     -7.549454519543    1    0    1
      0.000000000000      0.000000000000    -10.065939338757    1    0    1
      5.032969700311      0.000000000000    -10.065939338757    1    0    1
     10.065939338757      0.000000000000    -10.065939338757    1    0    1
      0.000000000000      7.117693980003    -10.065939338757    1    0    1
      5.032969700311      7.117693980003    -10.065939338757    1    0    1
     10.065939338757      7.117693980003    -10.065939338757    1    0    1
&END

↑

Vibrational analysis †

For the vibrational analysis, we need to construct a dynamical matrix and diagonalize it.

In the STATE run, we add the following line to perform the vibrational mode analysis.

TASK VIB

In addition, we need to create a file called `nfvibrate.data`.

Example of nfvibrate.data #1
```
    1  0.10D+01   1
 
      1   0.0200000000   0.0000000000   0.0000000000

    1 -0.10D+01   1
 
      1   0.0200000000   0.0000000000   0.0000000000
```
- line #1
```
    1  0.10D+01   1
```
  Column #1: number of atoms to be displaced
  Column #2: factor (magnitude) for the displacement
  Column #3: dummy variable
- line #2
```
      1   0.0200000000   0.0000000000   0.0000000000
```
  Column #1：atom index
  Column #2-4 displacement vector in the cartesian coordinate. Actual displacement is the vector multiplied by the factor (magnitude) specified in the line #1 ...
  All the necessary displacement vectors should be given in `nfvibrate.data`. Usually, we give a pair of plus and minus displacements.

Example of nfvibrate.data #2

    3  0.10D+01   1
 
      1   0.0018516229  -0.1016200502  -0.0086543879
      2   0.0042681410  -0.2329208549  -0.0086375658
      3   0.0003210803   0.0063360252  -0.0068488877

    3 -0.10D+01   1
 
      1   0.0018516229  -0.1016200502  -0.0086543879
      2   0.0042681410  -0.2329208549  -0.0086375658
      3   0.0003210803   0.0063360252  -0.0068488877

If nfvibrate.data is not found, `STATE` assumes that all the atoms are displaced, generates `nfvibrate.data`, and run the vibrational analysis. If you want to limit the number of displaced atoms, following option can be used:

&VIBRATION
 ATOM 1-3
&END

In this example, atoms #1, #2, and #3 are displaced. Currently, it is possible to specify the consecutive atoms, and therefore, if you want to displace a certain atoms, it is better to reorder the atomic positions, or otherwise you have to generate `nfvibrate.data` by yourself.

↑

Input file for the vibrational analysis. †

Below is an input file for the vibrational analysis, in which CO and Cu atom underneath is considered.

nfinp_vib

TASK         VIB
WF_OPT       DAV
NTYP         3
NATM         32
GMAX         6.00
GMAXP        20.00
KPOINT_MESH  4   4   1
KPOINT_SHIFT 1   1   0
NSTEP        200
MIX_ALPHA    0.30
SMEARING     MP
WIDTH        0.010
EDELTA       1.D-10
NEG          196
XCTYPE       vdW-DF2
ESM_BC       BC1
CPUMAX       1600.0
&VIBRATION
 ATOM 1-3
&END
&CELL
     15.098909039006      0.000000000000      0.000000000000
      0.000000000000     14.235387960000      0.000000000000
      0.000000000000      0.000000000000     50.329696796687
&END
&ATOMIC_SPECIES
 Cu  63.54000 pot.Cu_pbe1
 C   12.01115 pot.C_pbe1
 O   15.99940 pot.O_pbe1
&END
&ATOMIC_COORDINATES CARTESIAN
      0.000003823996     -0.000001138123      3.702323615193    1    1    2
      0.000010283052     -0.000006912305      5.897216927318    1    1    3
      0.000000351042     -0.000002382316      0.053467056659    1    1    1
      5.089242487895     -0.000001108633     -0.208242367820    1    1    1
     10.009661676277      0.000001103467     -0.208241073609    1    1    1
      0.000001196465      7.117696353327     -0.191027901816    1    1    1
      5.012492707154      7.117697566474     -0.167155951780    1    1    1
     10.086413584750      7.117696561458     -0.167155627900    1    1    1
      2.507494428154      3.538363991660     -2.421985716480    1    1    1
      7.549453707970      3.590875576905     -2.405963340815    1    1    1
     12.591415007976      3.538365483794     -2.421988185457    1    1    1
      2.507492583039     10.697023879015     -2.421990853447    1    1    1
      7.549453621923     10.644515276442     -2.405964405967    1    1    1
     12.591413959874     10.697024958358     -2.421982246650    1    1    1
      0.000000000000      0.000000000000     -5.032969700311    1    0    1
      5.032969700311      0.000000000000     -5.032969700311    1    0    1
     10.065939338757      0.000000000000     -5.032969700311    1    0    1
      0.000000000000      7.117693980003     -5.032969700311    1    0    1
      5.032969700311      7.117693980003     -5.032969700311    1    0    1
     10.065939338757      7.117693980003     -5.032969700311    1    0    1
      2.516484819239      3.558846990002     -7.549454519543    1    0    1
      7.549454519543      3.558846990002     -7.549454519543    1    0    1
     12.582424219851      3.558846990002     -7.549454519543    1    0    1
      2.516484819239     10.676540969990     -7.549454519543    1    0    1
      7.549454519543     10.676540969990     -7.549454519543    1    0    1
     12.582424219851     10.676540969990     -7.549454519543    1    0    1
      0.000000000000      0.000000000000    -10.065939338757    1    0    1
      5.032969700311      0.000000000000    -10.065939338757    1    0    1
     10.065939338757      0.000000000000    -10.065939338757    1    0    1
      0.000000000000      7.117693980003    -10.065939338757    1    0    1
      5.032969700311      7.117693980003    -10.065939338757    1    0    1
     10.065939338757      7.117693980003    -10.065939338757    1    0    1
&END

Note that you have to set the actual atomic mass for the vibrational analysis. This is different from the geometry optimization, in which we sometimes use artifical atomic masses.

↑

Restart †

In case all the calculations are not finished within the defined time, we need to restart the calculation. In such a case, use the keyword

RESTART

TASK RESTART_VIB

When you restart the calculation, new data (forces) will be appended to the exsisting nfforce.data. Please carefully check if the data `nfforce.data` is OK or not. Also, please make sure nfforce.data does not exist, when you start the vibrational analysis from scratch.

↑

Calculation of the vibrational frequencies using the GiF program †

Once all the calculations are done, it is possible to calculate the vibrational frequencies using the GiF program as follows.

gif -f nfforce.data

第一原理分子動力学プログラム STATE Senri Wiki

Menu