第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Crystal orbital overlap analysis (COOP) [#o37226be]
The crystal orbital overlap analysis (COOP) is a method t...
** Tutorial [#v7704f9e]
Let us use a CO molecule on a Pt(111) surface as an examp...
*** Preliminaries [#o403bbd6]
For the COOP calculation, we need the wave functions and ...
Input file for the SCF calculations of the combined syste...
1 0 0 0 0 0 : Pt(111)(sqrt(3)xs...
5.0000 15.0000 3 11 11 : gmax, gmaxp, ktyp...
1 0 : num_space_group, ...
Cartesian
7.914328000000 4.569339400000 0.00000000...
0.000000000000 9.138678810000 0.00000000...
0.000000000000 0.000000000000 38.77213053...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei...
-0.000000528145 -0.000042365186 3.76731167...
0.000000053537 0.000002980474 5.98634759...
0.000001949062 -0.000004500424 0.30414090...
2.638113295845 4.569319798127 -0.05741625...
5.276215081326 9.138653655057 -0.05741719...
0.000000331528 3.046226811762 -4.30299379...
2.638108391790 7.615566096905 -4.30299295...
5.276218871886 12.184904590329 -4.30299463...
0.000000000000 -3.046226270000 -8.61602901...
2.638109330000 1.523113130000 -8.61602901...
5.276218670000 6.092452540000 -8.61602901...
78.00 0.50 15.9994 1 1 0.0 : iatomn,alfa,amion...
6.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
8.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
0 0 0 0 0 : icond, inipos, in...
0 1 : ipre, ipri
1000 1000 0 60000.00 0 : nmd1,nmd2,last_it...
6 1 : way_mix mix_what
0 30 0.60 : iter_start, KBXMI...
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dtim3...
400.00 4 1 5.00D-12 : dtio ,imdalg, iex...
-0.0020 1.00D+03 0 : width,forccr,istr...
ggapbe 1 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4 : dummy
4 4 4 : dummy
64 : keg
1 : nextst
0 : dummy
2 : imsd
0 : evaluate_eko_diff
0 : npdosao
0 0.0
Input file for CO and Pt(111) are the followings.
CO (CO/nfinp_scf):
1 0 0 0 0 0 : CO molecule
5.0000 15.0000 3 2 2 : gmax, gmaxp, ktyp, ...
1 0 : num_space_group, ...
Cartesian
7.914328000000 4.569339400000 0.00000000...
0.000000000000 9.138678810000 0.00000000...
0.000000000000 0.000000000000 38.77213053...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei...
-0.000000528145 -0.000042365186 3.76731167...
0.000000053537 0.000002980474 5.98634759...
78.00 0.50 15.9994 1 1 0.0 : iatomn,alfa,amion...
6.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
8.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
0 0 0 0 0 : icond, inipos, in...
0 1 : ipre, ipri
1000 1000 0 60000.00 0 : nmd1,nmd2,last_it...
6 1 : way_mix mix_what
0 30 0.60 : iter_start, KBXMI...
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dtim3...
400.00 4 1 5.00D-12 : dtio ,imdalg, iex...
-0.0020 1.00D+03 0 : width,forccr,istr...
ggapbe 1 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4 : dummy
4 4 4 : dummy
8 : keg
1 : nextst
0 : dummy
2 : imsd
0 : evaluate_eko_diff
0 : npdosao
0 0.0
Pt (Pt/nfinp_scf):
1 0 0 0 0 0 : Pt(111)(sqrt(3)xs...
5.0000 15.0000 3 9 9 : gmax, gmaxp, ktyp...
1 0 : num_space_group, ...
Cartesian
7.914328000000 4.569339400000 0.00000000...
0.000000000000 9.138678810000 0.00000000...
0.000000000000 0.000000000000 38.77213053...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei...
0.000001949062 -0.000004500424 0.30414090...
2.638113295845 4.569319798127 -0.05741625...
5.276215081326 9.138653655057 -0.05741719...
0.000000331528 3.046226811762 -4.30299379...
2.638108391790 7.615566096905 -4.30299295...
5.276218871886 12.184904590329 -4.30299463...
0.000000000000 -3.046226270000 -8.61602901...
2.638109330000 1.523113130000 -8.61602901...
5.276218670000 6.092452540000 -8.61602901...
78.00 0.50 15.9994 1 1 0.0 : iatomn,alfa,amion...
6.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
8.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
0 0 0 0 0 : icond, inipos, in...
0 1 : ipre, ipri
1000 1000 0 60000.00 0 : nmd1,nmd2,last_it...
6 1 : way_mix mix_what
0 30 0.60 : iter_start, KBXMI...
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dtim3...
400.00 4 1 5.00D-12 : dtio ,imdalg, iex...
-0.0020 1.00D+03 0 : width,forccr,istr...
ggapbe 1 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4 : dummy
4 4 4 : dummy
56 : keg
1 : nextst
0 : dummy
2 : imsd
0 : evaluate_eko_diff
0 : npdosao
0 0.0
*** SCF [#y241c8c2]
In each subdirectories, perform SCF calculations to get C...
ln -s ../CO/zaj.data zak1.data
ln -s ../Pt/zaj.data zak3.data
Then create a file called nfcoop.data, which looks like
1 : KSPIN
20 : KNV3
8 8 2 14 : NPDOSMO1 KPDOSMO1 KATM1 KLMTA1
0 0 0 0 : NPDOSMO2 KPDOSMO2 KATM2 KLMTA2
56 56 9 180 : NPDOSMO3 KPDOSMO3 KATM3 KLMTA3
-15.0 5.0 0.1 2001 : EMIN EMAX EDELTA NPDOSE
Description of the variables:
-KSPIN: Number of spin components (1 for spin-unpolarized...
-KNV3: Number of k-points generated in the SCF
-NPDOSMO1: Number of bands (orbitals) for the subsystem #1
-KPDOSMO1: Maximum number of bands (orbitals) for the sub...
-KATM1: Number of atoms in the subsystem #1
-KLMTA1: Total number of projectors for the subsystem #1
-NPDOSMO2: Number of bands (orbitals) for the subsystem #...
-KPDOSMO2: Maximum number of bands (orbitals) for the sub...
-KATM2: Number of atoms in the subsystem #1 (if present, ...
-KLMTA2: Total number of projectors for the subsystem #2 ...
-NPDOSMO3: Number of bands (orbitals) for the subsystem #...
-KPDOSMO3: Maximum number of bands (orbitals) for the sub...
-KATM3: Number of atoms in the subsystem #3 (substrate)
-KLMTA3: Total number of projectors for the subsystem #3 ...
-EMIN: Minimum energy for DOS
-EMAX: Maximum energy for DOS
-DELTAE: Smearing width for DOS
-NPDOSE: Energy mesh (number of energy points should be N...
KLMTA* can be found in the STATE output files. Use grep t...
*** Overlap [#v8c8f855]
Having prepared zak1.data, zak3.data, and nfcoop.data, ex...
Further, use state2eg.pl (or state2eigen.pl) to extract t...
state2eigen.pl nfout_scf > eko.data
in the directory Total/.
The eigenvalue file should be always "eko.data" for the C...
*** COOP [#w629bf3e]
Finally, we use the program "coop_analysis" in the direct...
coop_analysis > coop.out
We get the densities of states projected onto the molecul...
PDOS can be extracted by executing
grep PDOS\: coop.out | awk -F\: '{print $2}' > pdos.dat
for GPOP and COOP
grep GPOP\: coop.out | awk -F\: '{print $2}' > gpop.dat
grep COOP\: coop.out | awk -F\: '{print $2}' > coop.dat
The format for PDOS, GPOP, and COOP is as follows
[Energy wrt Fermi level] [PDOS(MO#1)] [PDOS(MO#2)] [PDOS...
*** WARNING [#h40a24c7]
Note that one always has to use the reciprocal space form...
** References [#x8af4732]
- R. Hoffman, Mod. Phys. 60, 601 (1988).
- H. Aizawa and S. Tsuneyuki, Surf. Sci. 399, L364 (1998).
終了行:
* Crystal orbital overlap analysis (COOP) [#o37226be]
The crystal orbital overlap analysis (COOP) is a method t...
** Tutorial [#v7704f9e]
Let us use a CO molecule on a Pt(111) surface as an examp...
*** Preliminaries [#o403bbd6]
For the COOP calculation, we need the wave functions and ...
Input file for the SCF calculations of the combined syste...
1 0 0 0 0 0 : Pt(111)(sqrt(3)xs...
5.0000 15.0000 3 11 11 : gmax, gmaxp, ktyp...
1 0 : num_space_group, ...
Cartesian
7.914328000000 4.569339400000 0.00000000...
0.000000000000 9.138678810000 0.00000000...
0.000000000000 0.000000000000 38.77213053...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei...
-0.000000528145 -0.000042365186 3.76731167...
0.000000053537 0.000002980474 5.98634759...
0.000001949062 -0.000004500424 0.30414090...
2.638113295845 4.569319798127 -0.05741625...
5.276215081326 9.138653655057 -0.05741719...
0.000000331528 3.046226811762 -4.30299379...
2.638108391790 7.615566096905 -4.30299295...
5.276218871886 12.184904590329 -4.30299463...
0.000000000000 -3.046226270000 -8.61602901...
2.638109330000 1.523113130000 -8.61602901...
5.276218670000 6.092452540000 -8.61602901...
78.00 0.50 15.9994 1 1 0.0 : iatomn,alfa,amion...
6.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
8.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
0 0 0 0 0 : icond, inipos, in...
0 1 : ipre, ipri
1000 1000 0 60000.00 0 : nmd1,nmd2,last_it...
6 1 : way_mix mix_what
0 30 0.60 : iter_start, KBXMI...
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dtim3...
400.00 4 1 5.00D-12 : dtio ,imdalg, iex...
-0.0020 1.00D+03 0 : width,forccr,istr...
ggapbe 1 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4 : dummy
4 4 4 : dummy
64 : keg
1 : nextst
0 : dummy
2 : imsd
0 : evaluate_eko_diff
0 : npdosao
0 0.0
Input file for CO and Pt(111) are the followings.
CO (CO/nfinp_scf):
1 0 0 0 0 0 : CO molecule
5.0000 15.0000 3 2 2 : gmax, gmaxp, ktyp, ...
1 0 : num_space_group, ...
Cartesian
7.914328000000 4.569339400000 0.00000000...
0.000000000000 9.138678810000 0.00000000...
0.000000000000 0.000000000000 38.77213053...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei...
-0.000000528145 -0.000042365186 3.76731167...
0.000000053537 0.000002980474 5.98634759...
78.00 0.50 15.9994 1 1 0.0 : iatomn,alfa,amion...
6.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
8.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
0 0 0 0 0 : icond, inipos, in...
0 1 : ipre, ipri
1000 1000 0 60000.00 0 : nmd1,nmd2,last_it...
6 1 : way_mix mix_what
0 30 0.60 : iter_start, KBXMI...
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dtim3...
400.00 4 1 5.00D-12 : dtio ,imdalg, iex...
-0.0020 1.00D+03 0 : width,forccr,istr...
ggapbe 1 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4 : dummy
4 4 4 : dummy
8 : keg
1 : nextst
0 : dummy
2 : imsd
0 : evaluate_eko_diff
0 : npdosao
0 0.0
Pt (Pt/nfinp_scf):
1 0 0 0 0 0 : Pt(111)(sqrt(3)xs...
5.0000 15.0000 3 9 9 : gmax, gmaxp, ktyp...
1 0 : num_space_group, ...
Cartesian
7.914328000000 4.569339400000 0.00000000...
0.000000000000 9.138678810000 0.00000000...
0.000000000000 0.000000000000 38.77213053...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei...
0.000001949062 -0.000004500424 0.30414090...
2.638113295845 4.569319798127 -0.05741625...
5.276215081326 9.138653655057 -0.05741719...
0.000000331528 3.046226811762 -4.30299379...
2.638108391790 7.615566096905 -4.30299295...
5.276218871886 12.184904590329 -4.30299463...
0.000000000000 -3.046226270000 -8.61602901...
2.638109330000 1.523113130000 -8.61602901...
5.276218670000 6.092452540000 -8.61602901...
78.00 0.50 15.9994 1 1 0.0 : iatomn,alfa,amion...
6.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
8.00 0.15 15.9994 3 1 0.0 : iatomn,alfa,amion...
0 0 0 0 0 : icond, inipos, in...
0 1 : ipre, ipri
1000 1000 0 60000.00 0 : nmd1,nmd2,last_it...
6 1 : way_mix mix_what
0 30 0.60 : iter_start, KBXMI...
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dtim3...
400.00 4 1 5.00D-12 : dtio ,imdalg, iex...
-0.0020 1.00D+03 0 : width,forccr,istr...
ggapbe 1 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4 : dummy
4 4 4 : dummy
56 : keg
1 : nextst
0 : dummy
2 : imsd
0 : evaluate_eko_diff
0 : npdosao
0 0.0
*** SCF [#y241c8c2]
In each subdirectories, perform SCF calculations to get C...
ln -s ../CO/zaj.data zak1.data
ln -s ../Pt/zaj.data zak3.data
Then create a file called nfcoop.data, which looks like
1 : KSPIN
20 : KNV3
8 8 2 14 : NPDOSMO1 KPDOSMO1 KATM1 KLMTA1
0 0 0 0 : NPDOSMO2 KPDOSMO2 KATM2 KLMTA2
56 56 9 180 : NPDOSMO3 KPDOSMO3 KATM3 KLMTA3
-15.0 5.0 0.1 2001 : EMIN EMAX EDELTA NPDOSE
Description of the variables:
-KSPIN: Number of spin components (1 for spin-unpolarized...
-KNV3: Number of k-points generated in the SCF
-NPDOSMO1: Number of bands (orbitals) for the subsystem #1
-KPDOSMO1: Maximum number of bands (orbitals) for the sub...
-KATM1: Number of atoms in the subsystem #1
-KLMTA1: Total number of projectors for the subsystem #1
-NPDOSMO2: Number of bands (orbitals) for the subsystem #...
-KPDOSMO2: Maximum number of bands (orbitals) for the sub...
-KATM2: Number of atoms in the subsystem #1 (if present, ...
-KLMTA2: Total number of projectors for the subsystem #2 ...
-NPDOSMO3: Number of bands (orbitals) for the subsystem #...
-KPDOSMO3: Maximum number of bands (orbitals) for the sub...
-KATM3: Number of atoms in the subsystem #3 (substrate)
-KLMTA3: Total number of projectors for the subsystem #3 ...
-EMIN: Minimum energy for DOS
-EMAX: Maximum energy for DOS
-DELTAE: Smearing width for DOS
-NPDOSE: Energy mesh (number of energy points should be N...
KLMTA* can be found in the STATE output files. Use grep t...
*** Overlap [#v8c8f855]
Having prepared zak1.data, zak3.data, and nfcoop.data, ex...
Further, use state2eg.pl (or state2eigen.pl) to extract t...
state2eigen.pl nfout_scf > eko.data
in the directory Total/.
The eigenvalue file should be always "eko.data" for the C...
*** COOP [#w629bf3e]
Finally, we use the program "coop_analysis" in the direct...
coop_analysis > coop.out
We get the densities of states projected onto the molecul...
PDOS can be extracted by executing
grep PDOS\: coop.out | awk -F\: '{print $2}' > pdos.dat
for GPOP and COOP
grep GPOP\: coop.out | awk -F\: '{print $2}' > gpop.dat
grep COOP\: coop.out | awk -F\: '{print $2}' > coop.dat
The format for PDOS, GPOP, and COOP is as follows
[Energy wrt Fermi level] [PDOS(MO#1)] [PDOS(MO#2)] [PDOS...
*** WARNING [#h40a24c7]
Note that one always has to use the reciprocal space form...
** References [#x8af4732]
- R. Hoffman, Mod. Phys. 60, 601 (1988).
- H. Aizawa and S. Tsuneyuki, Surf. Sci. 399, L364 (1998).
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