第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Oxygen atom on an aluminum surface [#i1737eb4]
This tutorial explains how to perform scanning tunneling ...
In this example, instead of using a simple local density ...
** SCF calculation [#za8e048f]
Suppose the structure is fully optimized and a new input ...
- Pseudopotentials
-- Al_pbe1
-- O_pbe3
- Input file (nfinp_scf)
0 0 0 0 0 0 : Al(111) (3x3)
5.0 15.0 2 37 37 : GMAX GMAXP KTYP KATM KA...
1 0 : NUM_SPACE_GROUP TYPE
Cartesian
16.235313117399 0.000000000000 0.00000000...
8.117656558700 14.060193598063 0.00000000...
0.000000000000 0.000000000000 44.18692550...
4 4 1 1 1 1 : K_MESH
1 0 : NCORD NINV ...
2.705826513042 1.562208448277 1.54290425...
-0.101040174364 -0.058336519962 0.06175398...
5.512784204974 -0.058313698882 0.06174923...
10.823532872680 -0.010553333078 0.09332615...
2.705891678362 4.803367697679 0.06175126...
8.158736454981 4.710447914641 -0.15040889...
13.488359690248 4.710457156282 -0.15042116...
5.402626131859 9.378731841492 0.09332577...
10.823556250816 9.326033439020 -0.15042007...
16.244459949678 9.378743914505 0.09332468...
0.005685553104 3.121206464856 -4.44217939...
5.406084220392 3.121202931158 -4.44217457...
10.823537730940 3.082192093875 -4.50488202...
2.705880947950 7.818273168592 -4.43639249...
8.081025974571 7.832362395824 -4.50488176...
13.566048376540 7.832361823915 -4.50488610...
5.405657148113 12.494420562183 -4.43639048...
10.823544447840 12.504513279356 -4.44217975...
16.241420153507 12.494418723842 -4.43639251...
0.000000000000 -3.124487465505 -8.83738509...
5.411771037948 -3.124487465505 -8.83738509...
10.823542079420 -3.124487465505 -8.83738509...
2.705885520752 1.562243734036 -8.83738509...
8.117656558700 1.562243734036 -8.83738509...
13.529427596648 1.562243734036 -8.83738509...
5.411771037948 6.248974931245 -8.83738509...
10.823542079420 6.248974931245 -8.83738509...
16.235313117368 6.248974931245 -8.83738509...
0.000000000000 0.000000000000 -13.25607765...
5.411771037948 0.000000000000 -13.25607765...
10.823542079420 0.000000000000 -13.25607765...
2.705885520752 4.686731199776 -13.25607765...
8.117656558700 4.686731199776 -13.25607765...
13.529427596648 4.686731199776 -13.25607765...
5.411771037948 9.373462398956 -13.25607765...
10.823542079420 9.373462398956 -13.25607765...
16.235313117368 9.373462398956 -13.25607765...
13.0 0.5 26.982 1 1 0.0 : IATOMN ALFA AMIO...
8.0 0.5 15.999 3 1 0.0 : IATOMN ALFA AMIO...
0 0 0 0 0 : ICOND INIPOS INI...
0 1 : IPRE IPRI
200 1000 0 86400.00 0 : NMD1 NMD2 LAST_I...
6 1 : MIXWAY MIXWHAT
0 50 0.30 : ITER_START KBXMI...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTIM...
200.00 2 1 0.10D-08 : DTION IMDALG IEX...
-0.002 5.00D+03 0 : WIDTH FORCCR IST...
ggapbe 1 : XCTYPE KSPIN
1.00 : DESTM
102 : NBZTYP
4 4 4 : (DUMMY)
4 4 4 : (DUMMY)
68 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.0 : (DUMMY)
&ESM
BOUNDARY_CONDITION BARE
&END
Note for the STM simulation (and electronic structure ana...
4 4 1 1 1 1 : K_MESH
Note also when we perform a STM simulation, make sure tha...
&ESM
BOUNDARY_CONDITION BARE
&END
-Execution~
On the command line or in the job script, perform the fol...
$ mpirun -np 24 < nfinp_scf > nfout_scf
** Preparation of the STM simulation [#x9fdb7be]
Having obtained the self-consistent charge and potential,...
$ state2chgpro.sh nfout_scf > chgpro.dat
To generate a gnuplot script to plot the planar average o...
$ chgpro2plt chgpro.dat > chgpro.gp
and type
$ gnuplot chgpro.gp
To perform the STM simulation, the vacuum level needs to ...
This can be done by first executing
$ chgpro2vac -stm
Then we obtained a file "stm" is generated, which looks l...
&STM
STMOPT 1
Z0 14.11530000D0
VACUUM_LEVEL 0.00026382D0
&END
Here, Z0 indicate the z-coordinate at which the charge de...
This is copy-pasted in the input file for the STM simulat...
** STM simulation [#d700ec0c]
Having obtained self-consistent wave functions and vacuum...
- Input (nfinp_stm)
0 0 0 0 0 0 : Al(111) (3x3)
5.0 15.0 2 37 37 : GMAX GMAXP KTYP KATM KA...
1 0 : NUM_SPACE_GROUP TYPE
Cartesian
16.235313117399 0.000000000000 0.00000000...
8.117656558700 14.060193598063 0.00000000...
0.000000000000 0.000000000000 44.18692550...
4 4 1 1 1 1 : K_MESH
1 0 : NCORD NINV ...
2.705826513042 1.562208448277 1.54290425...
-0.101040174364 -0.058336519962 0.06175398...
5.512784204974 -0.058313698882 0.06174923...
10.823532872680 -0.010553333078 0.09332615...
2.705891678362 4.803367697679 0.06175126...
8.158736454981 4.710447914641 -0.15040889...
13.488359690248 4.710457156282 -0.15042116...
5.402626131859 9.378731841492 0.09332577...
10.823556250816 9.326033439020 -0.15042007...
16.244459949678 9.378743914505 0.09332468...
0.005685553104 3.121206464856 -4.44217939...
5.406084220392 3.121202931158 -4.44217457...
10.823537730940 3.082192093875 -4.50488202...
2.705880947950 7.818273168592 -4.43639249...
8.081025974571 7.832362395824 -4.50488176...
13.566048376540 7.832361823915 -4.50488610...
5.405657148113 12.494420562183 -4.43639048...
10.823544447840 12.504513279356 -4.44217975...
16.241420153507 12.494418723842 -4.43639251...
0.000000000000 -3.124487465505 -8.83738509...
5.411771037948 -3.124487465505 -8.83738509...
10.823542079420 -3.124487465505 -8.83738509...
2.705885520752 1.562243734036 -8.83738509...
8.117656558700 1.562243734036 -8.83738509...
13.529427596648 1.562243734036 -8.83738509...
5.411771037948 6.248974931245 -8.83738509...
10.823542079420 6.248974931245 -8.83738509...
16.235313117368 6.248974931245 -8.83738509...
0.000000000000 0.000000000000 -13.25607765...
5.411771037948 0.000000000000 -13.25607765...
10.823542079420 0.000000000000 -13.25607765...
2.705885520752 4.686731199776 -13.25607765...
8.117656558700 4.686731199776 -13.25607765...
13.529427596648 4.686731199776 -13.25607765...
5.411771037948 9.373462398956 -13.25607765...
10.823542079420 9.373462398956 -13.25607765...
16.235313117368 9.373462398956 -13.25607765...
13.0 0.5 26.982 1 1 0.0 : IATOMN ALFA AMIO...
8.0 0.5 15.999 3 1 0.0 : IATOMN ALFA AMIO...
21 0 0 0 0 : ICOND INIPOS INI...
0 1 : IPRE IPRI
200 1000 0 86400.00 0 : NMD1 NMD2 LAST_I...
6 1 : MIXWAY MIXWHAT
0 50 0.30 : ITER_START KBXMI...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTIM...
200.00 2 1 0.10D-08 : DTION IMDALG IEX...
-0.002 5.00D+03 0 : WIDTH FORCCR IST...
ggapbe 1 : XCTYPE KSPIN
0.10 : DESTM
102 : NBZTYP
4 4 4 : (DUMMY)
4 4 4 : (DUMMY)
68 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.0 : (DUMMY)
&ESM
BOUNDARY_CONDITION BARE
&END
&STM
STMOPT 1
Z0 14.11530000D0
VACUUM_LEVEL 0.00026382D0
BIAS 1.00
&END
This input file is exactly the same as that for SCF, exce...
21 0 0 0 0 : ICOND INIPOS INI...
where ICOND is set to 21 and the optional block
&STM
STMOPT 1
Z0 14.11530000D0
VACUUM_LEVEL 0.00026382D0
BIAS 1.00
&END
where Z0 and VACUUM_LEVEL are defined for the wave functi...
The bias is also set by using the keyword DESTM in the ma...
0.10 : DESTM
- Execution~
By using the above input, execute
$ mpirun -np 24 < nfinp_stm > nfout_stm
and we obtain "nfchgt_r.data", which contains the local d...
** Post processing [#d2a4892d]
We are almost there -- Let us use a utility program "chg2...
$ chg2xsf -i nfinp_dav -c nfchgt_r.data -p stm
and we obtain LDOS files in the XSF format named "stm_occ...
The height can be changed in graphic softwares such as XC...
Type
$ chg2xsf -h
for the usage of the chg2xsf program.~
To obtain a simulated image corresponding to a constant c...
$ chg2xsf -i nfinp_dav -c nfchgt_r.data -stm 1.e-8 -p stm
Here by adding the option "-stm 1.e-8", the chg2xsf gener...
** Excercise [#oa4c127e]
An STM simulation can be performed by using ICOND=10 (all...
** References [#l74fa56d]
- J. Tersoff and D. R. Hamann, Phys. Rev. Lett. 50, 1998 ...
- S. Heinze, S. Blugel, R. Pascal, M. Bode, and R. Wiesen...
- M. Rohfling, R. Temirov, F. S. Tautz, Phys. Rev. B 76, ...
- I. Hamada, R. Shimizu, T. Ohsawa, K. Iwaya, T. Hashizum...
終了行:
* Oxygen atom on an aluminum surface [#i1737eb4]
This tutorial explains how to perform scanning tunneling ...
In this example, instead of using a simple local density ...
** SCF calculation [#za8e048f]
Suppose the structure is fully optimized and a new input ...
- Pseudopotentials
-- Al_pbe1
-- O_pbe3
- Input file (nfinp_scf)
0 0 0 0 0 0 : Al(111) (3x3)
5.0 15.0 2 37 37 : GMAX GMAXP KTYP KATM KA...
1 0 : NUM_SPACE_GROUP TYPE
Cartesian
16.235313117399 0.000000000000 0.00000000...
8.117656558700 14.060193598063 0.00000000...
0.000000000000 0.000000000000 44.18692550...
4 4 1 1 1 1 : K_MESH
1 0 : NCORD NINV ...
2.705826513042 1.562208448277 1.54290425...
-0.101040174364 -0.058336519962 0.06175398...
5.512784204974 -0.058313698882 0.06174923...
10.823532872680 -0.010553333078 0.09332615...
2.705891678362 4.803367697679 0.06175126...
8.158736454981 4.710447914641 -0.15040889...
13.488359690248 4.710457156282 -0.15042116...
5.402626131859 9.378731841492 0.09332577...
10.823556250816 9.326033439020 -0.15042007...
16.244459949678 9.378743914505 0.09332468...
0.005685553104 3.121206464856 -4.44217939...
5.406084220392 3.121202931158 -4.44217457...
10.823537730940 3.082192093875 -4.50488202...
2.705880947950 7.818273168592 -4.43639249...
8.081025974571 7.832362395824 -4.50488176...
13.566048376540 7.832361823915 -4.50488610...
5.405657148113 12.494420562183 -4.43639048...
10.823544447840 12.504513279356 -4.44217975...
16.241420153507 12.494418723842 -4.43639251...
0.000000000000 -3.124487465505 -8.83738509...
5.411771037948 -3.124487465505 -8.83738509...
10.823542079420 -3.124487465505 -8.83738509...
2.705885520752 1.562243734036 -8.83738509...
8.117656558700 1.562243734036 -8.83738509...
13.529427596648 1.562243734036 -8.83738509...
5.411771037948 6.248974931245 -8.83738509...
10.823542079420 6.248974931245 -8.83738509...
16.235313117368 6.248974931245 -8.83738509...
0.000000000000 0.000000000000 -13.25607765...
5.411771037948 0.000000000000 -13.25607765...
10.823542079420 0.000000000000 -13.25607765...
2.705885520752 4.686731199776 -13.25607765...
8.117656558700 4.686731199776 -13.25607765...
13.529427596648 4.686731199776 -13.25607765...
5.411771037948 9.373462398956 -13.25607765...
10.823542079420 9.373462398956 -13.25607765...
16.235313117368 9.373462398956 -13.25607765...
13.0 0.5 26.982 1 1 0.0 : IATOMN ALFA AMIO...
8.0 0.5 15.999 3 1 0.0 : IATOMN ALFA AMIO...
0 0 0 0 0 : ICOND INIPOS INI...
0 1 : IPRE IPRI
200 1000 0 86400.00 0 : NMD1 NMD2 LAST_I...
6 1 : MIXWAY MIXWHAT
0 50 0.30 : ITER_START KBXMI...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTIM...
200.00 2 1 0.10D-08 : DTION IMDALG IEX...
-0.002 5.00D+03 0 : WIDTH FORCCR IST...
ggapbe 1 : XCTYPE KSPIN
1.00 : DESTM
102 : NBZTYP
4 4 4 : (DUMMY)
4 4 4 : (DUMMY)
68 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.0 : (DUMMY)
&ESM
BOUNDARY_CONDITION BARE
&END
Note for the STM simulation (and electronic structure ana...
4 4 1 1 1 1 : K_MESH
Note also when we perform a STM simulation, make sure tha...
&ESM
BOUNDARY_CONDITION BARE
&END
-Execution~
On the command line or in the job script, perform the fol...
$ mpirun -np 24 < nfinp_scf > nfout_scf
** Preparation of the STM simulation [#x9fdb7be]
Having obtained the self-consistent charge and potential,...
$ state2chgpro.sh nfout_scf > chgpro.dat
To generate a gnuplot script to plot the planar average o...
$ chgpro2plt chgpro.dat > chgpro.gp
and type
$ gnuplot chgpro.gp
To perform the STM simulation, the vacuum level needs to ...
This can be done by first executing
$ chgpro2vac -stm
Then we obtained a file "stm" is generated, which looks l...
&STM
STMOPT 1
Z0 14.11530000D0
VACUUM_LEVEL 0.00026382D0
&END
Here, Z0 indicate the z-coordinate at which the charge de...
This is copy-pasted in the input file for the STM simulat...
** STM simulation [#d700ec0c]
Having obtained self-consistent wave functions and vacuum...
- Input (nfinp_stm)
0 0 0 0 0 0 : Al(111) (3x3)
5.0 15.0 2 37 37 : GMAX GMAXP KTYP KATM KA...
1 0 : NUM_SPACE_GROUP TYPE
Cartesian
16.235313117399 0.000000000000 0.00000000...
8.117656558700 14.060193598063 0.00000000...
0.000000000000 0.000000000000 44.18692550...
4 4 1 1 1 1 : K_MESH
1 0 : NCORD NINV ...
2.705826513042 1.562208448277 1.54290425...
-0.101040174364 -0.058336519962 0.06175398...
5.512784204974 -0.058313698882 0.06174923...
10.823532872680 -0.010553333078 0.09332615...
2.705891678362 4.803367697679 0.06175126...
8.158736454981 4.710447914641 -0.15040889...
13.488359690248 4.710457156282 -0.15042116...
5.402626131859 9.378731841492 0.09332577...
10.823556250816 9.326033439020 -0.15042007...
16.244459949678 9.378743914505 0.09332468...
0.005685553104 3.121206464856 -4.44217939...
5.406084220392 3.121202931158 -4.44217457...
10.823537730940 3.082192093875 -4.50488202...
2.705880947950 7.818273168592 -4.43639249...
8.081025974571 7.832362395824 -4.50488176...
13.566048376540 7.832361823915 -4.50488610...
5.405657148113 12.494420562183 -4.43639048...
10.823544447840 12.504513279356 -4.44217975...
16.241420153507 12.494418723842 -4.43639251...
0.000000000000 -3.124487465505 -8.83738509...
5.411771037948 -3.124487465505 -8.83738509...
10.823542079420 -3.124487465505 -8.83738509...
2.705885520752 1.562243734036 -8.83738509...
8.117656558700 1.562243734036 -8.83738509...
13.529427596648 1.562243734036 -8.83738509...
5.411771037948 6.248974931245 -8.83738509...
10.823542079420 6.248974931245 -8.83738509...
16.235313117368 6.248974931245 -8.83738509...
0.000000000000 0.000000000000 -13.25607765...
5.411771037948 0.000000000000 -13.25607765...
10.823542079420 0.000000000000 -13.25607765...
2.705885520752 4.686731199776 -13.25607765...
8.117656558700 4.686731199776 -13.25607765...
13.529427596648 4.686731199776 -13.25607765...
5.411771037948 9.373462398956 -13.25607765...
10.823542079420 9.373462398956 -13.25607765...
16.235313117368 9.373462398956 -13.25607765...
13.0 0.5 26.982 1 1 0.0 : IATOMN ALFA AMIO...
8.0 0.5 15.999 3 1 0.0 : IATOMN ALFA AMIO...
21 0 0 0 0 : ICOND INIPOS INI...
0 1 : IPRE IPRI
200 1000 0 86400.00 0 : NMD1 NMD2 LAST_I...
6 1 : MIXWAY MIXWHAT
0 50 0.30 : ITER_START KBXMI...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTIM...
200.00 2 1 0.10D-08 : DTION IMDALG IEX...
-0.002 5.00D+03 0 : WIDTH FORCCR IST...
ggapbe 1 : XCTYPE KSPIN
0.10 : DESTM
102 : NBZTYP
4 4 4 : (DUMMY)
4 4 4 : (DUMMY)
68 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.0 : (DUMMY)
&ESM
BOUNDARY_CONDITION BARE
&END
&STM
STMOPT 1
Z0 14.11530000D0
VACUUM_LEVEL 0.00026382D0
BIAS 1.00
&END
This input file is exactly the same as that for SCF, exce...
21 0 0 0 0 : ICOND INIPOS INI...
where ICOND is set to 21 and the optional block
&STM
STMOPT 1
Z0 14.11530000D0
VACUUM_LEVEL 0.00026382D0
BIAS 1.00
&END
where Z0 and VACUUM_LEVEL are defined for the wave functi...
The bias is also set by using the keyword DESTM in the ma...
0.10 : DESTM
- Execution~
By using the above input, execute
$ mpirun -np 24 < nfinp_stm > nfout_stm
and we obtain "nfchgt_r.data", which contains the local d...
** Post processing [#d2a4892d]
We are almost there -- Let us use a utility program "chg2...
$ chg2xsf -i nfinp_dav -c nfchgt_r.data -p stm
and we obtain LDOS files in the XSF format named "stm_occ...
The height can be changed in graphic softwares such as XC...
Type
$ chg2xsf -h
for the usage of the chg2xsf program.~
To obtain a simulated image corresponding to a constant c...
$ chg2xsf -i nfinp_dav -c nfchgt_r.data -stm 1.e-8 -p stm
Here by adding the option "-stm 1.e-8", the chg2xsf gener...
** Excercise [#oa4c127e]
An STM simulation can be performed by using ICOND=10 (all...
** References [#l74fa56d]
- J. Tersoff and D. R. Hamann, Phys. Rev. Lett. 50, 1998 ...
- S. Heinze, S. Blugel, R. Pascal, M. Bode, and R. Wiesen...
- M. Rohfling, R. Temirov, F. S. Tautz, Phys. Rev. B 76, ...
- I. Hamada, R. Shimizu, T. Ohsawa, K. Iwaya, T. Hashizum...
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