第一原理分子動力学プログラム STATE Senri Wiki
開始行:
*Cl on Al(100) [#od195485]
In this example, geometry optimization of Cl atom on Al(1...
The surface is modeled by a three-layer slab with the sur...
This is followed by vibrational mode analysis of the adso...
**Geometry optimization [#g5e21d8d]
- Input file (nfinp_1)
1 0 0 0 0 0
4.00 10.00 2 7 7 : GMAX GMAXP...
1 0 : NUMBER OF S...
CARTESIAN
7.6534000000 0.0000000000 00.0000000000 ...
0.0000000000 7.6534000000 00.0000000000 ...
00.0000000000 00.0000000000 30.6136000000 ...
4 4 1 2 2 1 : KNX KNY KNZ...
1 0 : NCORD NINV
0.0000000000 3.8267000000 4.0000000000 ...
0.0000000000 3.8267000000 0.0000000000 ...
3.8267000000 0.0000000000 0.0000000000 ...
0.0000000000 0.0000000000 -3.8267000000 ...
3.8267000000 3.8267000000 -3.8267000000 ...
0.0000000000 3.8267000000 -7.6534000000 ...
3.8267000000 0.0000000000 -7.6534000000 ...
13 0.15 26.9815 3 1 0.00 : IATOMN ALFA...
17 0.15 35.4527 3 1 0.00 : IATOMN ALFA...
0 0 0 0 0 : ICOND INIPO...
0 1 : IPRE IPRI
100 200 0 57200.00 0 : NMD1 NMD2 I...
3 1 : WAY_MIX MIX...
0 20 0.8 : STARTING_MI...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM2...
600.00 4 1 0.10D-08 : DTIO IMDALG...
-0.002 0.10D-02 0 : WIDTH FORCC...
ggapbe 1 : XCTYPE NSPIN
1.00 : DESTM N_STM
101 : NBZTYP
0 0 0 : NKX NKY N...
0 0 0 : NKX2 NKY2 N...
16 : NEG
1 : NEXTST(MB)
0 : DUMMY
2 : IMSD
0 : EVALUATE_EK...
0 : NPDOSAO
0 0.00
- Job script (qsub1.sh)
#$ -S /bin/sh
#$ -cwd
#$ -pe fillup 6
#$ -N Al100-Cl
#disable OPENMP parallelism
OMP_NUM_THREADS=1
# execuable of the STATE code
ln -fs ../../../src/STATE
# pseudopotential data
ln -fs ${HOME}/STATE/gncpp/pot.Al_pbe1 fort.37
ln -fs ${HOME}/STATE/gncpp/pot.Cl_pbe1 fort.38
# launch STATE
mpirun -np $NSLOTS ./STATE < nfinp_1 > nfout_1
- Output file (nfout_1)~
The maximum force is monitored by
$ grep -A1 f_max nfout_1
and get
NIT TotalEnergy f_max f_rms edel ...
1 -27.41198444 0.017835 0.015239 0.20D-09 0....
--
...
--
NIT TotalEnergy f_max f_rms edel ...
16 -27.41380898 0.002821 0.001976 0.25D-09 0....
--
NIT TotalEnergy f_max f_rms edel ...
17 -27.41384275 0.000594 0.000369 0.54D-09 0....
Use the geometry written in GEOMETRY to generate a new in...
** Vibrational mode analysis [#kfb7b4a0]
- Input file (nfinp_2)
1 0 0 0 0 0
4.00 10.00 2 7 7 : GMAX GMAXP...
1 0 : NUMBER OF S...
CARTESIAN
7.6534000000 0.0000000000 00.0000000000
0.0000000000 7.6534000000 00.0000000000
00.0000000000 00.0000000000 30.6136000000
4 4 1 2 2 1 : KNX KNY KNZ...
1 0 : NCORD NINV
-0.000000251836 3.826701578025 4.04961960...
-0.000001836163 3.826699462952 -0.04577218...
3.826699127649 0.000000430959 -0.23360604...
0.000000000000 0.000000000000 -3.82670000...
3.826700000000 3.826700000000 -3.82670000...
0.000000000000 3.826700000000 -7.65340000...
3.826700000000 0.000000000000 -7.65340000...
13 0.15 26.9815 3 1 0.00 : IATOMN ALFA...
17 0.15 35.4527 3 1 0.00 : IATOMN ALFA...
0 0 0 0 0 : ICOND INIPO...
0 1 : IPRE IPRI
100 200 0 57200.00 0 : NMD1 NMD2 I...
3 1 : WAY_MIX MIX...
0 20 0.8 : STARTING_MI...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM2...
600.00 3 1 0.10D-08 : DTIO IMDALG...
-0.002 0.10D-02 0 : WIDTH FORCC...
ggapbe 1 : XCTYPE NSPIN
1.00 : DESTM N_STM
101 : NBZTYP
0 0 0 : NKX NKY N...
0 0 0 : NKX2 NKY2 N...
16 : NEG
1 : NEXTST(MB)
0 : DUMMY
2 : IMSD
0 : EVALUATE_EK...
0 : NPDOSAO
0 0.00
For the vibrational mode analysis, use IMDALG=3. In addit...
-nfvibrate.data
1 1.0d0
1 0.0000000000 0.0000000000 0.000000000000
1 1.0d0
1 0.1000000000 0.0000000000 0.000000000000
1 -1.0d0
1 0.1000000000 0.0000000000 0.000000000000
1 1.0d0
1 0.0000000000 0.1000000000 0.000000000000
1 -1.0d0
1 0.0000000000 0.1000000000 0.000000000000
1 1.0d0
1 0.0000000000 0.0000000000 0.100000000000
1 -1.0d0
1 0.0000000000 0.0000000000 0.100000000000
The format is as follows
[index for the displacement (dummy)] [factor for the dis...
[index for the displaced atom #1] [X displacement] [Y di...
...
[index for the displaced atom #N] [X displacement] [Y di...
[index for the displacement (dummy)] [factor for the dis...
[index for the displaced atom #2] [X displacement] [Y di...
...
[index for the displaced atom #N] [X displacement] [Y di...
...
Atomic displacements are defined by the given displacemen...
In this example, the first displacement is zero, to check...
The vibration of the adsorbed Cl atom is considered and t...
- Job script (qsub.sh)
#$ -S /bin/sh
#$ -cwd
#$ -pe fillup 6
#$ -N Al100-Cl
#disable OPENMP parallelism
OMP_NUM_THREADS=1
# execuable of the STATE code
ln -fs ../../../src/STATE
# pseudopotential data
ln -fs ${HOME}/STATE/gncpp/pot.Al_pbe1 fort.37
ln -fs ${HOME}/STATE/gncpp/pot.Cl_pbe1 fort.38
# launch STATE
mpirun -np $NSLOTS ./STATE < nfinp_2 > nfout_2
- Output file (nfout_2)~
To calculate the vibrational frequencies, the forces shou...
To do so, util/state2md.sh is used. In this example,
$ ../util/state2md.sh nfout_2 > MD_2.dat
to get "MD_2.dat." Further, we need to edit "MD_2.dat" to...
7 3
36 27 27 27 27 27 27
2
1 0.100000 3.826702 4.049620 -0.00005 -0...
2 -0.000002 3.826699 -0.045772 -0.00043 0...
3 3.826699 0.000000 -0.233606 0.00033 -0...
4 0.000000 0.000000 -3.826700 0.00021 -0...
5 3.826700 3.826700 -3.826700 -0.00005 0...
6 0.000000 3.826700 -7.653400 0.00020 0...
7 3.826700 0.000000 -7.653400 -0.00021 -0...
...
The first and second columns in the first line indicate t...
Then use the program "gif" to calculate the vibrational f...
This can be done by performing
$ ../../util/Vibration/src/gif < MD_2.dat > MD_2.out
The vibrational frequency can be found in "MD_2.out" as
=======
SUMMARY
=======
MODE WR : NU(meV) NU(cm-1)
1 0.14D-04 : 2.37 19.09
2 0.14D-04 : 2.37 19.09
3 0.36D-02 : 38.15 307.73
Normal modes are printed in the standard output as well a...
終了行:
*Cl on Al(100) [#od195485]
In this example, geometry optimization of Cl atom on Al(1...
The surface is modeled by a three-layer slab with the sur...
This is followed by vibrational mode analysis of the adso...
**Geometry optimization [#g5e21d8d]
- Input file (nfinp_1)
1 0 0 0 0 0
4.00 10.00 2 7 7 : GMAX GMAXP...
1 0 : NUMBER OF S...
CARTESIAN
7.6534000000 0.0000000000 00.0000000000 ...
0.0000000000 7.6534000000 00.0000000000 ...
00.0000000000 00.0000000000 30.6136000000 ...
4 4 1 2 2 1 : KNX KNY KNZ...
1 0 : NCORD NINV
0.0000000000 3.8267000000 4.0000000000 ...
0.0000000000 3.8267000000 0.0000000000 ...
3.8267000000 0.0000000000 0.0000000000 ...
0.0000000000 0.0000000000 -3.8267000000 ...
3.8267000000 3.8267000000 -3.8267000000 ...
0.0000000000 3.8267000000 -7.6534000000 ...
3.8267000000 0.0000000000 -7.6534000000 ...
13 0.15 26.9815 3 1 0.00 : IATOMN ALFA...
17 0.15 35.4527 3 1 0.00 : IATOMN ALFA...
0 0 0 0 0 : ICOND INIPO...
0 1 : IPRE IPRI
100 200 0 57200.00 0 : NMD1 NMD2 I...
3 1 : WAY_MIX MIX...
0 20 0.8 : STARTING_MI...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM2...
600.00 4 1 0.10D-08 : DTIO IMDALG...
-0.002 0.10D-02 0 : WIDTH FORCC...
ggapbe 1 : XCTYPE NSPIN
1.00 : DESTM N_STM
101 : NBZTYP
0 0 0 : NKX NKY N...
0 0 0 : NKX2 NKY2 N...
16 : NEG
1 : NEXTST(MB)
0 : DUMMY
2 : IMSD
0 : EVALUATE_EK...
0 : NPDOSAO
0 0.00
- Job script (qsub1.sh)
#$ -S /bin/sh
#$ -cwd
#$ -pe fillup 6
#$ -N Al100-Cl
#disable OPENMP parallelism
OMP_NUM_THREADS=1
# execuable of the STATE code
ln -fs ../../../src/STATE
# pseudopotential data
ln -fs ${HOME}/STATE/gncpp/pot.Al_pbe1 fort.37
ln -fs ${HOME}/STATE/gncpp/pot.Cl_pbe1 fort.38
# launch STATE
mpirun -np $NSLOTS ./STATE < nfinp_1 > nfout_1
- Output file (nfout_1)~
The maximum force is monitored by
$ grep -A1 f_max nfout_1
and get
NIT TotalEnergy f_max f_rms edel ...
1 -27.41198444 0.017835 0.015239 0.20D-09 0....
--
...
--
NIT TotalEnergy f_max f_rms edel ...
16 -27.41380898 0.002821 0.001976 0.25D-09 0....
--
NIT TotalEnergy f_max f_rms edel ...
17 -27.41384275 0.000594 0.000369 0.54D-09 0....
Use the geometry written in GEOMETRY to generate a new in...
** Vibrational mode analysis [#kfb7b4a0]
- Input file (nfinp_2)
1 0 0 0 0 0
4.00 10.00 2 7 7 : GMAX GMAXP...
1 0 : NUMBER OF S...
CARTESIAN
7.6534000000 0.0000000000 00.0000000000
0.0000000000 7.6534000000 00.0000000000
00.0000000000 00.0000000000 30.6136000000
4 4 1 2 2 1 : KNX KNY KNZ...
1 0 : NCORD NINV
-0.000000251836 3.826701578025 4.04961960...
-0.000001836163 3.826699462952 -0.04577218...
3.826699127649 0.000000430959 -0.23360604...
0.000000000000 0.000000000000 -3.82670000...
3.826700000000 3.826700000000 -3.82670000...
0.000000000000 3.826700000000 -7.65340000...
3.826700000000 0.000000000000 -7.65340000...
13 0.15 26.9815 3 1 0.00 : IATOMN ALFA...
17 0.15 35.4527 3 1 0.00 : IATOMN ALFA...
0 0 0 0 0 : ICOND INIPO...
0 1 : IPRE IPRI
100 200 0 57200.00 0 : NMD1 NMD2 I...
3 1 : WAY_MIX MIX...
0 20 0.8 : STARTING_MI...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM2...
600.00 3 1 0.10D-08 : DTIO IMDALG...
-0.002 0.10D-02 0 : WIDTH FORCC...
ggapbe 1 : XCTYPE NSPIN
1.00 : DESTM N_STM
101 : NBZTYP
0 0 0 : NKX NKY N...
0 0 0 : NKX2 NKY2 N...
16 : NEG
1 : NEXTST(MB)
0 : DUMMY
2 : IMSD
0 : EVALUATE_EK...
0 : NPDOSAO
0 0.00
For the vibrational mode analysis, use IMDALG=3. In addit...
-nfvibrate.data
1 1.0d0
1 0.0000000000 0.0000000000 0.000000000000
1 1.0d0
1 0.1000000000 0.0000000000 0.000000000000
1 -1.0d0
1 0.1000000000 0.0000000000 0.000000000000
1 1.0d0
1 0.0000000000 0.1000000000 0.000000000000
1 -1.0d0
1 0.0000000000 0.1000000000 0.000000000000
1 1.0d0
1 0.0000000000 0.0000000000 0.100000000000
1 -1.0d0
1 0.0000000000 0.0000000000 0.100000000000
The format is as follows
[index for the displacement (dummy)] [factor for the dis...
[index for the displaced atom #1] [X displacement] [Y di...
...
[index for the displaced atom #N] [X displacement] [Y di...
[index for the displacement (dummy)] [factor for the dis...
[index for the displaced atom #2] [X displacement] [Y di...
...
[index for the displaced atom #N] [X displacement] [Y di...
...
Atomic displacements are defined by the given displacemen...
In this example, the first displacement is zero, to check...
The vibration of the adsorbed Cl atom is considered and t...
- Job script (qsub.sh)
#$ -S /bin/sh
#$ -cwd
#$ -pe fillup 6
#$ -N Al100-Cl
#disable OPENMP parallelism
OMP_NUM_THREADS=1
# execuable of the STATE code
ln -fs ../../../src/STATE
# pseudopotential data
ln -fs ${HOME}/STATE/gncpp/pot.Al_pbe1 fort.37
ln -fs ${HOME}/STATE/gncpp/pot.Cl_pbe1 fort.38
# launch STATE
mpirun -np $NSLOTS ./STATE < nfinp_2 > nfout_2
- Output file (nfout_2)~
To calculate the vibrational frequencies, the forces shou...
To do so, util/state2md.sh is used. In this example,
$ ../util/state2md.sh nfout_2 > MD_2.dat
to get "MD_2.dat." Further, we need to edit "MD_2.dat" to...
7 3
36 27 27 27 27 27 27
2
1 0.100000 3.826702 4.049620 -0.00005 -0...
2 -0.000002 3.826699 -0.045772 -0.00043 0...
3 3.826699 0.000000 -0.233606 0.00033 -0...
4 0.000000 0.000000 -3.826700 0.00021 -0...
5 3.826700 3.826700 -3.826700 -0.00005 0...
6 0.000000 3.826700 -7.653400 0.00020 0...
7 3.826700 0.000000 -7.653400 -0.00021 -0...
...
The first and second columns in the first line indicate t...
Then use the program "gif" to calculate the vibrational f...
This can be done by performing
$ ../../util/Vibration/src/gif < MD_2.dat > MD_2.out
The vibrational frequency can be found in "MD_2.out" as
=======
SUMMARY
=======
MODE WR : NU(meV) NU(cm-1)
1 0.14D-04 : 2.37 19.09
2 0.14D-04 : 2.37 19.09
3 0.36D-02 : 38.15 307.73
Normal modes are printed in the standard output as well a...
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