第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* CO/Cu(110)Interface [#x577f6fb]
#Contents
** Introduction [#z3a5c3bb]
In this document, how to perform the vibrational analysis...
Here, in addition to the adsorbed CO molecule, the Cu ato...
The system is modeled using a 4-layer Cu(110) slab.
Below is the input file of a CO adsorbed Cu(110) surface,...
CO molecule and Cu atoms in the first and second layers o...
** Input file [#l3f09e64]
- ''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 0.00000000...
0.000000000000 14.235387960000 0.00000000...
0.000000000000 0.000000000000 50.32969679...
&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 3.70232361...
0.000010283052 -0.000006912305 5.89721692...
0.000000351042 -0.000002382316 0.05346705...
5.089242487895 -0.000001108633 -0.20824236...
10.009661676277 0.000001103467 -0.20824107...
0.000001196465 7.117696353327 -0.19102790...
5.012492707154 7.117697566474 -0.16715595...
10.086413584750 7.117696561458 -0.16715562...
2.507494428154 3.538363991660 -2.42198571...
7.549453707970 3.590875576905 -2.40596334...
12.591415007976 3.538365483794 -2.42198818...
2.507492583039 10.697023879015 -2.42199085...
7.549453621923 10.644515276442 -2.40596440...
12.591413959874 10.697024958358 -2.42198224...
0.000000000000 0.000000000000 -5.03296970...
5.032969700311 0.000000000000 -5.03296970...
10.065939338757 0.000000000000 -5.03296970...
0.000000000000 7.117693980003 -5.03296970...
5.032969700311 7.117693980003 -5.03296970...
10.065939338757 7.117693980003 -5.03296970...
2.516484819239 3.558846990002 -7.54945451...
7.549454519543 3.558846990002 -7.54945451...
12.582424219851 3.558846990002 -7.54945451...
2.516484819239 10.676540969990 -7.54945451...
7.549454519543 10.676540969990 -7.54945451...
12.582424219851 10.676540969990 -7.54945451...
0.000000000000 0.000000000000 -10.06593933...
5.032969700311 0.000000000000 -10.06593933...
10.065939338757 0.000000000000 -10.06593933...
0.000000000000 7.117693980003 -10.06593933...
5.032969700311 7.117693980003 -10.06593933...
10.065939338757 7.117693980003 -10.06593933...
&END
** Vibrational analysis [#l50a32b0]
For the vibrational analysis, we need to construct a dyna...
In the STATE run, we add the following line to perform th...
TASK VIB
In addition, we need to create a file called `nfvibrate.d...
-- 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 coordina...
...~
All the necessary displacement vectors should be given in...
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 ...
If you want to limit the number of displaced atoms, follo...
&VIBRATION
ATOM 1-3
&END
In this example, atoms #1, #2, and #3 are displaced.
Currently, it is possible to specify the consecutive atom...
*** Input file for the vibrational analysis. [#y00e141f]
Below is an input file for the vibrational analysis, in w...
- ''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 0.00000000...
0.000000000000 14.235387960000 0.00000000...
0.000000000000 0.000000000000 50.32969679...
&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 3.70232361...
0.000010283052 -0.000006912305 5.89721692...
0.000000351042 -0.000002382316 0.05346705...
5.089242487895 -0.000001108633 -0.20824236...
10.009661676277 0.000001103467 -0.20824107...
0.000001196465 7.117696353327 -0.19102790...
5.012492707154 7.117697566474 -0.16715595...
10.086413584750 7.117696561458 -0.16715562...
2.507494428154 3.538363991660 -2.42198571...
7.549453707970 3.590875576905 -2.40596334...
12.591415007976 3.538365483794 -2.42198818...
2.507492583039 10.697023879015 -2.42199085...
7.549453621923 10.644515276442 -2.40596440...
12.591413959874 10.697024958358 -2.42198224...
0.000000000000 0.000000000000 -5.03296970...
5.032969700311 0.000000000000 -5.03296970...
10.065939338757 0.000000000000 -5.03296970...
0.000000000000 7.117693980003 -5.03296970...
5.032969700311 7.117693980003 -5.03296970...
10.065939338757 7.117693980003 -5.03296970...
2.516484819239 3.558846990002 -7.54945451...
7.549454519543 3.558846990002 -7.54945451...
12.582424219851 3.558846990002 -7.54945451...
2.516484819239 10.676540969990 -7.54945451...
7.549454519543 10.676540969990 -7.54945451...
12.582424219851 10.676540969990 -7.54945451...
0.000000000000 0.000000000000 -10.06593933...
5.032969700311 0.000000000000 -10.06593933...
10.065939338757 0.000000000000 -10.06593933...
0.000000000000 7.117693980003 -10.06593933...
5.032969700311 7.117693980003 -10.06593933...
10.065939338757 7.117693980003 -10.06593933...
&END
COLOR(red){Note that you have to set the actual atomic ma...
*** Restart [#n51b8c96]
In case all the calculations are not finished within the ...
In such a case, use the keyword
RESTART
Or
TASK RESTART_VIB
When you restart the calculation, new data (forces) will ...
Also, please make sure ''nfforce.data'' does not exist, w...
*** Calculation of the vibrational frequencies using the ...
Once all the calculations are done, it is possible to cal...
gif -f nfforce.data
終了行:
* CO/Cu(110)Interface [#x577f6fb]
#Contents
** Introduction [#z3a5c3bb]
In this document, how to perform the vibrational analysis...
Here, in addition to the adsorbed CO molecule, the Cu ato...
The system is modeled using a 4-layer Cu(110) slab.
Below is the input file of a CO adsorbed Cu(110) surface,...
CO molecule and Cu atoms in the first and second layers o...
** Input file [#l3f09e64]
- ''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 0.00000000...
0.000000000000 14.235387960000 0.00000000...
0.000000000000 0.000000000000 50.32969679...
&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 3.70232361...
0.000010283052 -0.000006912305 5.89721692...
0.000000351042 -0.000002382316 0.05346705...
5.089242487895 -0.000001108633 -0.20824236...
10.009661676277 0.000001103467 -0.20824107...
0.000001196465 7.117696353327 -0.19102790...
5.012492707154 7.117697566474 -0.16715595...
10.086413584750 7.117696561458 -0.16715562...
2.507494428154 3.538363991660 -2.42198571...
7.549453707970 3.590875576905 -2.40596334...
12.591415007976 3.538365483794 -2.42198818...
2.507492583039 10.697023879015 -2.42199085...
7.549453621923 10.644515276442 -2.40596440...
12.591413959874 10.697024958358 -2.42198224...
0.000000000000 0.000000000000 -5.03296970...
5.032969700311 0.000000000000 -5.03296970...
10.065939338757 0.000000000000 -5.03296970...
0.000000000000 7.117693980003 -5.03296970...
5.032969700311 7.117693980003 -5.03296970...
10.065939338757 7.117693980003 -5.03296970...
2.516484819239 3.558846990002 -7.54945451...
7.549454519543 3.558846990002 -7.54945451...
12.582424219851 3.558846990002 -7.54945451...
2.516484819239 10.676540969990 -7.54945451...
7.549454519543 10.676540969990 -7.54945451...
12.582424219851 10.676540969990 -7.54945451...
0.000000000000 0.000000000000 -10.06593933...
5.032969700311 0.000000000000 -10.06593933...
10.065939338757 0.000000000000 -10.06593933...
0.000000000000 7.117693980003 -10.06593933...
5.032969700311 7.117693980003 -10.06593933...
10.065939338757 7.117693980003 -10.06593933...
&END
** Vibrational analysis [#l50a32b0]
For the vibrational analysis, we need to construct a dyna...
In the STATE run, we add the following line to perform th...
TASK VIB
In addition, we need to create a file called `nfvibrate.d...
-- 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 coordina...
...~
All the necessary displacement vectors should be given in...
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 ...
If you want to limit the number of displaced atoms, follo...
&VIBRATION
ATOM 1-3
&END
In this example, atoms #1, #2, and #3 are displaced.
Currently, it is possible to specify the consecutive atom...
*** Input file for the vibrational analysis. [#y00e141f]
Below is an input file for the vibrational analysis, in w...
- ''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 0.00000000...
0.000000000000 14.235387960000 0.00000000...
0.000000000000 0.000000000000 50.32969679...
&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 3.70232361...
0.000010283052 -0.000006912305 5.89721692...
0.000000351042 -0.000002382316 0.05346705...
5.089242487895 -0.000001108633 -0.20824236...
10.009661676277 0.000001103467 -0.20824107...
0.000001196465 7.117696353327 -0.19102790...
5.012492707154 7.117697566474 -0.16715595...
10.086413584750 7.117696561458 -0.16715562...
2.507494428154 3.538363991660 -2.42198571...
7.549453707970 3.590875576905 -2.40596334...
12.591415007976 3.538365483794 -2.42198818...
2.507492583039 10.697023879015 -2.42199085...
7.549453621923 10.644515276442 -2.40596440...
12.591413959874 10.697024958358 -2.42198224...
0.000000000000 0.000000000000 -5.03296970...
5.032969700311 0.000000000000 -5.03296970...
10.065939338757 0.000000000000 -5.03296970...
0.000000000000 7.117693980003 -5.03296970...
5.032969700311 7.117693980003 -5.03296970...
10.065939338757 7.117693980003 -5.03296970...
2.516484819239 3.558846990002 -7.54945451...
7.549454519543 3.558846990002 -7.54945451...
12.582424219851 3.558846990002 -7.54945451...
2.516484819239 10.676540969990 -7.54945451...
7.549454519543 10.676540969990 -7.54945451...
12.582424219851 10.676540969990 -7.54945451...
0.000000000000 0.000000000000 -10.06593933...
5.032969700311 0.000000000000 -10.06593933...
10.065939338757 0.000000000000 -10.06593933...
0.000000000000 7.117693980003 -10.06593933...
5.032969700311 7.117693980003 -10.06593933...
10.065939338757 7.117693980003 -10.06593933...
&END
COLOR(red){Note that you have to set the actual atomic ma...
*** Restart [#n51b8c96]
In case all the calculations are not finished within the ...
In such a case, use the keyword
RESTART
Or
TASK RESTART_VIB
When you restart the calculation, new data (forces) will ...
Also, please make sure ''nfforce.data'' does not exist, w...
*** Calculation of the vibrational frequencies using the ...
Once all the calculations are done, it is possible to cal...
gif -f nfforce.data
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