第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* hfacH molecule on a nickel surface [#u7088cb3]
This tutorial explains how to perform the crystal orbital...
** Preliminary [#v100fd4a]
In the COOP calculation, the wave function of the total s...
Thus, we need to prepare wave functions for the subsystem.
In the present system, we prepare wave functions of molec...
- STATE version
-- 5.6.3
- Pseudopotentials
-- Ni_pbe4
-- F_pbe1
-- C_pbe1
-- O_pbe1
-- H_lda1
** SCF calculations [#r2b0be49]
We first relax the system and create a new input file usi...
We also create input files for subsystem using the optimi...
The input files for the combined system and subsystems ar...
- ./nfinp_1 (combined system)
0 0 0 0 0 0 : Ni ( 4L + 16L )
6.0000 20.0000 5 63 63 : gmax, gmaxp, ktyp,...
1 0 : num_space_group, type
Cartesian
18.853223409384 0.000000000000 0.00000000...
0.000000000000 19.996863180000 0.00000000...
0.000000000000 0.000000000000 47.13305852...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei,imdtyp,ityp
3.996033909759 6.423162152279 7.52298940...
4.633918309151 7.123379460829 5.10601370...
3.635103884227 5.253332343494 3.14693187...
4.731721715104 2.690776174457 3.32389224...
3.200483027950 0.471065818069 3.52902965...
4.120907476388 -1.686820049470 5.18800070...
3.410025784713 -1.291010684906 7.64845235...
3.138910721527 -3.990404972103 4.49640968...
6.710352133631 -1.907538456185 5.16740177...
0.630361749489 0.637068850434 3.37384350...
0.931152312144 5.345290940286 3.26461679...
3.688095192120 9.504638201919 4.74880843...
7.235648802353 7.279856147374 5.03116219...
6.667976160760 2.610581848382 4.03966005...
0.357655206834 3.440269198314 3.39159220...
-4.723393044566 -6.659760068776 -0.24417648...
-4.766966242109 -0.002829325009 -0.23705514...
-4.743794937018 6.656139747554 -0.23588005...
-0.011608354807 -6.657491571052 -0.27001726...
-0.053793076202 -0.046032678740 -0.14047252...
0.004101946979 6.632961379942 -0.13266538...
4.698813209313 -6.654695829816 -0.25182888...
4.685756715949 0.294502803370 0.00710342...
4.659328430105 6.502758307018 -0.18231636...
9.406005430046 -6.657768212578 -0.24743699...
9.413612628005 0.025443431192 -0.23571239...
9.405185522265 6.655221273086 -0.22742074...
-2.362387725422 -3.315354047591 -2.38560505...
-2.372460657256 3.324479261331 -2.40669672...
-2.353468393749 9.967108679099 -2.35143554...
2.380240190019 -3.280084445723 -2.39287972...
2.318083997074 3.323346703637 -2.58003852...
2.362350188616 9.975604524032 -2.39436457...
7.032730190885 -3.270921711124 -2.32994047...
7.102040811859 3.341277167718 -2.47673332...
7.048003975979 9.969771766060 -2.35194644...
11.759975516057 -3.327723005070 -2.36052332...
11.784484202409 3.338143705962 -2.38694403...
11.771270751385 9.995685282686 -2.35038759...
-4.713305852300 -6.665621060000 -4.71330585...
-4.713305852300 0.000000000000 -4.71330585...
-4.713305852300 6.665621060000 -4.71330585...
0.000000000000 -6.665621060000 -4.71330585...
0.000000000000 0.000000000000 -4.71330585...
0.000000000000 6.665621060000 -4.71330585...
4.713305852300 -6.665621060000 -4.71330585...
4.713305852300 0.000000000000 -4.71330585...
4.713305852300 6.665621060000 -4.71330585...
9.426611704700 -6.665621060000 -4.71330585...
9.426611704700 0.000000000000 -4.71330585...
9.426611704700 6.665621060000 -4.71330585...
-2.356652926200 -3.332810530000 -7.06995877...
-2.356652926200 3.332810530000 -7.06995877...
-2.356652926200 9.998431590000 -7.06995877...
2.356652926200 -3.332810530000 -7.06995877...
2.356652926200 3.332810530000 -7.06995877...
2.356652926200 9.998431590000 -7.06995877...
7.069958778500 -3.332810530000 -7.06995877...
7.069958778500 3.332810530000 -7.06995877...
7.069958778500 9.998431590000 -7.06995877...
11.783264630900 -3.332810530000 -7.06995877...
11.783264630900 3.332810530000 -7.06995877...
11.783264630900 9.998431590000 -7.06995877...
28 0.5000 58.710 1 1 0.2 : IATOMN ALFA AM...
9 0.5000 18.998 1 1 0.2 : IATOMN ALFA AM...
6 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
8 0.5000 15.999 1 1 0.2 : IATOMN ALFA AM...
1 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
0 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
0 1 : ipre, ipri
0400 1000 0 420000.00 0 : nmd1,nmd2,last_iter,...
6 1 : SIMPLE=1,BROYD1=2,BROYD2=3,DFP=4,P...
0 30 0.10 : iter_start, KBXMIX, MIX_ALPHA
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dt...
200.00 6 1 1.00D-10 : dtio ,imdalg, ...
-0.0010 1.00D+03 0 : width,forccr,i...
rev-vdW-DF2 2 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4
4 4 4
384 : keg
1 : nextst(mb)
0 : 0 random numbers 1: matrix
2 : imsd 1=MSD, 2=Preconditioned
0 : evaluate_eko_diff
0 : npdosao
0 0.0
2 : mvelsc
300.0D0 30.0D0 30 1.0D0 : tempw,tolp,nro...
500.0D0 8 15 1 : wnosep,nhc,nos...
5.0D-8 : frict
0 : mcnstr
DIST 1 3 1.83401
DIST 2 3 1.83401
BEND 1 3 2 104.23195
&ESM
BOUNDARY_CONDITION BARE
&END
- HFACH/nfinp_1 (adsorbate)
0 0 0 0 0 0 : Ni ( 4L + 16L )
6.0000 20.0000 5 15 15 : gmax, gmaxp, ktyp,...
1 0 : num_space_group, type
Cartesian
18.853223409384 0.000000000000 0.00000000...
0.000000000000 19.996863180000 0.00000000...
0.000000000000 0.000000000000 47.13305852...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei,imdtyp,ityp
3.996033909759 6.423162152279 7.52298940...
4.633918309151 7.123379460829 5.10601370...
3.635103884227 5.253332343494 3.14693187...
4.731721715104 2.690776174457 3.32389224...
3.200483027950 0.471065818069 3.52902965...
4.120907476388 -1.686820049470 5.18800070...
3.410025784713 -1.291010684906 7.64845235...
3.138910721527 -3.990404972103 4.49640968...
6.710352133631 -1.907538456185 5.16740177...
0.630361749489 0.637068850434 3.37384350...
0.931152312144 5.345290940286 3.26461679...
3.688095192120 9.504638201919 4.74880843...
7.235648802353 7.279856147374 5.03116219...
6.667976160760 2.610581848382 4.03966005...
0.357655206834 3.440269198314 3.39159220...
28 0.5000 58.710 1 1 0.2 : IATOMN ALFA AM...
9 0.5000 18.998 1 1 0.2 : IATOMN ALFA AM...
6 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
8 0.5000 15.999 1 1 0.2 : IATOMN ALFA AM...
1 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
0 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
0 1 : ipre, ipri
0400 1000 0 420000.00 0 : nmd1,nmd2,last_iter,...
6 1 : SIMPLE=1,BROYD1=2,BROYD2=3,DFP=4,P...
0 30 0.10 : iter_start, KBXMIX, MIX_ALPHA
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dt...
200.00 6 1 1.00D-10 : dtio ,imdalg, ...
-0.0010 1.00D+03 0 : width,forccr,i...
rev-vdW-DF2 2 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4
4 4 4
48 : keg
1 : nextst(mb)
0 : 0 random numbers 1: matrix
2 : imsd 1=MSD, 2=Preconditioned
0 : evaluate_eko_diff
0 : npdosao
0 0.0
2 : mvelsc
300.0D0 30.0D0 30 1.0D0 : tempw,tolp,nro...
500.0D0 8 15 1 : wnosep,nhc,nos...
5.0D-8 : frict
0 : mcnstr
DIST 1 3 1.83401
DIST 2 3 1.83401
BEND 1 3 2 104.23195
&ESM
BOUNDARY_CONDITION BARE
&END
- Ni/nfinp_1 (substrate)
0 0 0 0 0 0 : Ni ( 4L + 16L )
6.0000 20.0000 5 48 48 : gmax, gmaxp, ktyp,...
1 0 : num_space_group, type
Cartesian
18.853223409384 0.000000000000 0.00000000...
0.000000000000 19.996863180000 0.00000000...
0.000000000000 0.000000000000 47.13305852...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei,imdtyp,ityp
-4.723393044566 -6.659760068776 -0.24417648...
-4.766966242109 -0.002829325009 -0.23705514...
-4.743794937018 6.656139747554 -0.23588005...
-0.011608354807 -6.657491571052 -0.27001726...
-0.053793076202 -0.046032678740 -0.14047252...
0.004101946979 6.632961379942 -0.13266538...
4.698813209313 -6.654695829816 -0.25182888...
4.685756715949 0.294502803370 0.00710342...
4.659328430105 6.502758307018 -0.18231636...
9.406005430046 -6.657768212578 -0.24743699...
9.413612628005 0.025443431192 -0.23571239...
9.405185522265 6.655221273086 -0.22742074...
-2.362387725422 -3.315354047591 -2.38560505...
-2.372460657256 3.324479261331 -2.40669672...
-2.353468393749 9.967108679099 -2.35143554...
2.380240190019 -3.280084445723 -2.39287972...
2.318083997074 3.323346703637 -2.58003852...
2.362350188616 9.975604524032 -2.39436457...
7.032730190885 -3.270921711124 -2.32994047...
7.102040811859 3.341277167718 -2.47673332...
7.048003975979 9.969771766060 -2.35194644...
11.759975516057 -3.327723005070 -2.36052332...
11.784484202409 3.338143705962 -2.38694403...
11.771270751385 9.995685282686 -2.35038759...
-4.713305852300 -6.665621060000 -4.71330585...
-4.713305852300 0.000000000000 -4.71330585...
-4.713305852300 6.665621060000 -4.71330585...
0.000000000000 -6.665621060000 -4.71330585...
0.000000000000 0.000000000000 -4.71330585...
0.000000000000 6.665621060000 -4.71330585...
4.713305852300 -6.665621060000 -4.71330585...
4.713305852300 0.000000000000 -4.71330585...
4.713305852300 6.665621060000 -4.71330585...
9.426611704700 -6.665621060000 -4.71330585...
9.426611704700 0.000000000000 -4.71330585...
9.426611704700 6.665621060000 -4.71330585...
-2.356652926200 -3.332810530000 -7.06995877...
-2.356652926200 3.332810530000 -7.06995877...
-2.356652926200 9.998431590000 -7.06995877...
2.356652926200 -3.332810530000 -7.06995877...
2.356652926200 3.332810530000 -7.06995877...
2.356652926200 9.998431590000 -7.06995877...
7.069958778500 -3.332810530000 -7.06995877...
7.069958778500 3.332810530000 -7.06995877...
7.069958778500 9.998431590000 -7.06995877...
11.783264630900 -3.332810530000 -7.06995877...
11.783264630900 3.332810530000 -7.06995877...
11.783264630900 9.998431590000 -7.06995877...
28 0.5000 58.710 1 1 0.2 : IATOMN ALFA AM...
9 0.5000 18.998 1 1 0.2 : IATOMN ALFA AM...
6 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
8 0.5000 15.999 1 1 0.2 : IATOMN ALFA AM...
1 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
0 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
0 1 : ipre, ipri
0400 1000 0 420000.00 0 : nmd1,nmd2,last_iter,...
6 1 : SIMPLE=1,BROYD1=2,BROYD2=3,DFP=4,P...
0 30 0.10 : iter_start, KBXMIX, MIX_ALPHA
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dt...
200.00 6 1 1.00D-10 : dtio ,imdalg, ...
-0.0010 1.00D+03 0 : width,forccr,i...
rev-vdW-DF2 2 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4
4 4 4
336 : keg
1 : nextst(mb)
0 : 0 random numbers 1: matrix
2 : imsd 1=MSD, 2=Preconditioned
0 : evaluate_eko_diff
0 : npdosao
0 0.0
2 : mvelsc
300.0D0 30.0D0 30 1.0D0 : tempw,tolp,nro...
500.0D0 8 15 1 : wnosep,nhc,nos...
5.0D-8 : frict
0 : mcnstr
DIST 1 3 1.83401
DIST 2 3 1.83401
BEND 1 3 2 104.23195
&ESM
BOUNDARY_CONDITION BARE
&END
In the current working directory, perform the following o...
- Combined system
$ mpirun -np 24 ./STATE < nfinp_1 > nfout_1
- Adsorbate
$ cd HFACH
$ mpirun -np 24 ./STATE < nfinp_1 > nfout_1
- Substrate
$ cd ../Ni
$ mpirun -np 24 ./STATE < nfinp_1 > nfout_1
** Prep of the COOP analysis [#ga0e82af]
After converging all the wave functions (./zaj.data, HFAC...
First, create a symbolic links in the current working dir...
$ ln -s HFACH/zaj.data zak1.data
$ ln -s Ni/zaj.data zak3.data
and then create a new input file for the preparation.
Let us copy nfinp_1 to nfinp_coop
$ cp nfinp_1 nfinp_coop
and change ICOND from 0 to 17 in nfinp_coop as
17 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
Furthermore, we need to create 'nfcoop.data' to set the c...
'nfcoop.data' may look like:
2 : KSPIN
40 : KNV3
43 48 15 101 : NPDOSMO1 KPDOSMO1 KATM1 ...
0 0 0 0 : NPDOSMO2 KPDOSMO2 KATM2 ...
336 336 48 864 : NPDOSMO3 KPDOSMO3 KATM3 ...
-15.0 5.0 0.5 2001 : EMIN EMAX EWIDTH NPDOSE
Having prepared "nfcoop.data", execute STATE using nfinp_...
$ mpirun -np 24 ./STATE < nfinp_coop > nfout_coop
Finally, we need to prepare 'eko.data', a file containing...
$ state2eigen.pl nfout_1 > eko.data
** COOP analysis [#x19d8dda]
When all the preliminary calculations are successfully pe...
- coop.data
- coop_bij.data
- coop_sij.data
- eko.data
- nfcoop.data
and we are ready to perform COOP analysis!
Assuming the command search path for the COOP program ('c...
$ coop_analysis > coop.out
and densities of states (DOSs) projected onto the molecul...
To extract MOPDOSs, type
$ grep 'PDOS\:' coop.out | awk -F\: '{print $2}' > pdos....
To extract COOPs, type
$ grep 'COOP2\:' coop.out | awk -F\: '{print $2}' > coop...
In the current example, the system is spin polarized, and...
For convenience, we split them as follows:
$ wc -l pdos.dat
4006 pdos.dat
$ split -l 2003 pdos.dat; mv xaa pdos_up.dat; mv xab pdo...
$ wc -l coop2.dat
4006 coop2.dat
$ split -l 2003 coop2.dat; mv xaa coop2_up.dat; mv xab c...
Those files (pdos.dat/coop2.dat) contain energy and DOS d...
- 1st column: energy with respect to the Fermi level (in ...
- 2nd - NPDOSMO1 column (2nd - 1st MO, 3rd - 2nd MO, 4th ...
Then, spin-up MOPDOS for HOMO, LUMO, and LUMO+1 may be pl...
> plot 'pdos_up.dat' using ($1):($39) title 'HOMO ' wit...
'' using ($1):($40) title 'LUMO ' with...
'' using ($1):($41) title 'LUMO+1' with...
and spin-up COOP for HOMO (orbital #38), LUMO (orbital #3...
> plot 'coop2_up.dat' using ($1):($39) title 'HOMO ' wi...
'' using ($1):($40) title 'LUMO ' wi...
'' using ($1):($41) title 'LUMO+1' wi...
considering that HOMO is the 38th orbital in the current ...
** References [#t5c09734]
-R. Hoffmann, Rev. Mod. Phys. 60, 601 (1988).
-H. Aizawa and S. Tsuneyuki, Surf. Sci. 399, L364 (1998).
終了行:
* hfacH molecule on a nickel surface [#u7088cb3]
This tutorial explains how to perform the crystal orbital...
** Preliminary [#v100fd4a]
In the COOP calculation, the wave function of the total s...
Thus, we need to prepare wave functions for the subsystem.
In the present system, we prepare wave functions of molec...
- STATE version
-- 5.6.3
- Pseudopotentials
-- Ni_pbe4
-- F_pbe1
-- C_pbe1
-- O_pbe1
-- H_lda1
** SCF calculations [#r2b0be49]
We first relax the system and create a new input file usi...
We also create input files for subsystem using the optimi...
The input files for the combined system and subsystems ar...
- ./nfinp_1 (combined system)
0 0 0 0 0 0 : Ni ( 4L + 16L )
6.0000 20.0000 5 63 63 : gmax, gmaxp, ktyp,...
1 0 : num_space_group, type
Cartesian
18.853223409384 0.000000000000 0.00000000...
0.000000000000 19.996863180000 0.00000000...
0.000000000000 0.000000000000 47.13305852...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei,imdtyp,ityp
3.996033909759 6.423162152279 7.52298940...
4.633918309151 7.123379460829 5.10601370...
3.635103884227 5.253332343494 3.14693187...
4.731721715104 2.690776174457 3.32389224...
3.200483027950 0.471065818069 3.52902965...
4.120907476388 -1.686820049470 5.18800070...
3.410025784713 -1.291010684906 7.64845235...
3.138910721527 -3.990404972103 4.49640968...
6.710352133631 -1.907538456185 5.16740177...
0.630361749489 0.637068850434 3.37384350...
0.931152312144 5.345290940286 3.26461679...
3.688095192120 9.504638201919 4.74880843...
7.235648802353 7.279856147374 5.03116219...
6.667976160760 2.610581848382 4.03966005...
0.357655206834 3.440269198314 3.39159220...
-4.723393044566 -6.659760068776 -0.24417648...
-4.766966242109 -0.002829325009 -0.23705514...
-4.743794937018 6.656139747554 -0.23588005...
-0.011608354807 -6.657491571052 -0.27001726...
-0.053793076202 -0.046032678740 -0.14047252...
0.004101946979 6.632961379942 -0.13266538...
4.698813209313 -6.654695829816 -0.25182888...
4.685756715949 0.294502803370 0.00710342...
4.659328430105 6.502758307018 -0.18231636...
9.406005430046 -6.657768212578 -0.24743699...
9.413612628005 0.025443431192 -0.23571239...
9.405185522265 6.655221273086 -0.22742074...
-2.362387725422 -3.315354047591 -2.38560505...
-2.372460657256 3.324479261331 -2.40669672...
-2.353468393749 9.967108679099 -2.35143554...
2.380240190019 -3.280084445723 -2.39287972...
2.318083997074 3.323346703637 -2.58003852...
2.362350188616 9.975604524032 -2.39436457...
7.032730190885 -3.270921711124 -2.32994047...
7.102040811859 3.341277167718 -2.47673332...
7.048003975979 9.969771766060 -2.35194644...
11.759975516057 -3.327723005070 -2.36052332...
11.784484202409 3.338143705962 -2.38694403...
11.771270751385 9.995685282686 -2.35038759...
-4.713305852300 -6.665621060000 -4.71330585...
-4.713305852300 0.000000000000 -4.71330585...
-4.713305852300 6.665621060000 -4.71330585...
0.000000000000 -6.665621060000 -4.71330585...
0.000000000000 0.000000000000 -4.71330585...
0.000000000000 6.665621060000 -4.71330585...
4.713305852300 -6.665621060000 -4.71330585...
4.713305852300 0.000000000000 -4.71330585...
4.713305852300 6.665621060000 -4.71330585...
9.426611704700 -6.665621060000 -4.71330585...
9.426611704700 0.000000000000 -4.71330585...
9.426611704700 6.665621060000 -4.71330585...
-2.356652926200 -3.332810530000 -7.06995877...
-2.356652926200 3.332810530000 -7.06995877...
-2.356652926200 9.998431590000 -7.06995877...
2.356652926200 -3.332810530000 -7.06995877...
2.356652926200 3.332810530000 -7.06995877...
2.356652926200 9.998431590000 -7.06995877...
7.069958778500 -3.332810530000 -7.06995877...
7.069958778500 3.332810530000 -7.06995877...
7.069958778500 9.998431590000 -7.06995877...
11.783264630900 -3.332810530000 -7.06995877...
11.783264630900 3.332810530000 -7.06995877...
11.783264630900 9.998431590000 -7.06995877...
28 0.5000 58.710 1 1 0.2 : IATOMN ALFA AM...
9 0.5000 18.998 1 1 0.2 : IATOMN ALFA AM...
6 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
8 0.5000 15.999 1 1 0.2 : IATOMN ALFA AM...
1 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
0 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
0 1 : ipre, ipri
0400 1000 0 420000.00 0 : nmd1,nmd2,last_iter,...
6 1 : SIMPLE=1,BROYD1=2,BROYD2=3,DFP=4,P...
0 30 0.10 : iter_start, KBXMIX, MIX_ALPHA
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dt...
200.00 6 1 1.00D-10 : dtio ,imdalg, ...
-0.0010 1.00D+03 0 : width,forccr,i...
rev-vdW-DF2 2 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4
4 4 4
384 : keg
1 : nextst(mb)
0 : 0 random numbers 1: matrix
2 : imsd 1=MSD, 2=Preconditioned
0 : evaluate_eko_diff
0 : npdosao
0 0.0
2 : mvelsc
300.0D0 30.0D0 30 1.0D0 : tempw,tolp,nro...
500.0D0 8 15 1 : wnosep,nhc,nos...
5.0D-8 : frict
0 : mcnstr
DIST 1 3 1.83401
DIST 2 3 1.83401
BEND 1 3 2 104.23195
&ESM
BOUNDARY_CONDITION BARE
&END
- HFACH/nfinp_1 (adsorbate)
0 0 0 0 0 0 : Ni ( 4L + 16L )
6.0000 20.0000 5 15 15 : gmax, gmaxp, ktyp,...
1 0 : num_space_group, type
Cartesian
18.853223409384 0.000000000000 0.00000000...
0.000000000000 19.996863180000 0.00000000...
0.000000000000 0.000000000000 47.13305852...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei,imdtyp,ityp
3.996033909759 6.423162152279 7.52298940...
4.633918309151 7.123379460829 5.10601370...
3.635103884227 5.253332343494 3.14693187...
4.731721715104 2.690776174457 3.32389224...
3.200483027950 0.471065818069 3.52902965...
4.120907476388 -1.686820049470 5.18800070...
3.410025784713 -1.291010684906 7.64845235...
3.138910721527 -3.990404972103 4.49640968...
6.710352133631 -1.907538456185 5.16740177...
0.630361749489 0.637068850434 3.37384350...
0.931152312144 5.345290940286 3.26461679...
3.688095192120 9.504638201919 4.74880843...
7.235648802353 7.279856147374 5.03116219...
6.667976160760 2.610581848382 4.03966005...
0.357655206834 3.440269198314 3.39159220...
28 0.5000 58.710 1 1 0.2 : IATOMN ALFA AM...
9 0.5000 18.998 1 1 0.2 : IATOMN ALFA AM...
6 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
8 0.5000 15.999 1 1 0.2 : IATOMN ALFA AM...
1 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
0 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
0 1 : ipre, ipri
0400 1000 0 420000.00 0 : nmd1,nmd2,last_iter,...
6 1 : SIMPLE=1,BROYD1=2,BROYD2=3,DFP=4,P...
0 30 0.10 : iter_start, KBXMIX, MIX_ALPHA
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dt...
200.00 6 1 1.00D-10 : dtio ,imdalg, ...
-0.0010 1.00D+03 0 : width,forccr,i...
rev-vdW-DF2 2 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4
4 4 4
48 : keg
1 : nextst(mb)
0 : 0 random numbers 1: matrix
2 : imsd 1=MSD, 2=Preconditioned
0 : evaluate_eko_diff
0 : npdosao
0 0.0
2 : mvelsc
300.0D0 30.0D0 30 1.0D0 : tempw,tolp,nro...
500.0D0 8 15 1 : wnosep,nhc,nos...
5.0D-8 : frict
0 : mcnstr
DIST 1 3 1.83401
DIST 2 3 1.83401
BEND 1 3 2 104.23195
&ESM
BOUNDARY_CONDITION BARE
&END
- Ni/nfinp_1 (substrate)
0 0 0 0 0 0 : Ni ( 4L + 16L )
6.0000 20.0000 5 48 48 : gmax, gmaxp, ktyp,...
1 0 : num_space_group, type
Cartesian
18.853223409384 0.000000000000 0.00000000...
0.000000000000 19.996863180000 0.00000000...
0.000000000000 0.000000000000 47.13305852...
06 06 01 1 1 1 : K_mesh
1 0 : ncord,ninv : iwei,imdtyp,ityp
-4.723393044566 -6.659760068776 -0.24417648...
-4.766966242109 -0.002829325009 -0.23705514...
-4.743794937018 6.656139747554 -0.23588005...
-0.011608354807 -6.657491571052 -0.27001726...
-0.053793076202 -0.046032678740 -0.14047252...
0.004101946979 6.632961379942 -0.13266538...
4.698813209313 -6.654695829816 -0.25182888...
4.685756715949 0.294502803370 0.00710342...
4.659328430105 6.502758307018 -0.18231636...
9.406005430046 -6.657768212578 -0.24743699...
9.413612628005 0.025443431192 -0.23571239...
9.405185522265 6.655221273086 -0.22742074...
-2.362387725422 -3.315354047591 -2.38560505...
-2.372460657256 3.324479261331 -2.40669672...
-2.353468393749 9.967108679099 -2.35143554...
2.380240190019 -3.280084445723 -2.39287972...
2.318083997074 3.323346703637 -2.58003852...
2.362350188616 9.975604524032 -2.39436457...
7.032730190885 -3.270921711124 -2.32994047...
7.102040811859 3.341277167718 -2.47673332...
7.048003975979 9.969771766060 -2.35194644...
11.759975516057 -3.327723005070 -2.36052332...
11.784484202409 3.338143705962 -2.38694403...
11.771270751385 9.995685282686 -2.35038759...
-4.713305852300 -6.665621060000 -4.71330585...
-4.713305852300 0.000000000000 -4.71330585...
-4.713305852300 6.665621060000 -4.71330585...
0.000000000000 -6.665621060000 -4.71330585...
0.000000000000 0.000000000000 -4.71330585...
0.000000000000 6.665621060000 -4.71330585...
4.713305852300 -6.665621060000 -4.71330585...
4.713305852300 0.000000000000 -4.71330585...
4.713305852300 6.665621060000 -4.71330585...
9.426611704700 -6.665621060000 -4.71330585...
9.426611704700 0.000000000000 -4.71330585...
9.426611704700 6.665621060000 -4.71330585...
-2.356652926200 -3.332810530000 -7.06995877...
-2.356652926200 3.332810530000 -7.06995877...
-2.356652926200 9.998431590000 -7.06995877...
2.356652926200 -3.332810530000 -7.06995877...
2.356652926200 3.332810530000 -7.06995877...
2.356652926200 9.998431590000 -7.06995877...
7.069958778500 -3.332810530000 -7.06995877...
7.069958778500 3.332810530000 -7.06995877...
7.069958778500 9.998431590000 -7.06995877...
11.783264630900 -3.332810530000 -7.06995877...
11.783264630900 3.332810530000 -7.06995877...
11.783264630900 9.998431590000 -7.06995877...
28 0.5000 58.710 1 1 0.2 : IATOMN ALFA AM...
9 0.5000 18.998 1 1 0.2 : IATOMN ALFA AM...
6 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
8 0.5000 15.999 1 1 0.2 : IATOMN ALFA AM...
1 0.5000 12.011 1 1 0.2 : IATOMN ALFA AM...
0 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
0 1 : ipre, ipri
0400 1000 0 420000.00 0 : nmd1,nmd2,last_iter,...
6 1 : SIMPLE=1,BROYD1=2,BROYD2=3,DFP=4,P...
0 30 0.10 : iter_start, KBXMIX, MIX_ALPHA
0.20 0.30 0.20 0.20 0.20 : dtim1,dtim2,dt...
200.00 6 1 1.00D-10 : dtio ,imdalg, ...
-0.0010 1.00D+03 0 : width,forccr,i...
rev-vdW-DF2 2 : xctype,kspin
1.00 : destm
101 : nbztyp
4 4 4
4 4 4
336 : keg
1 : nextst(mb)
0 : 0 random numbers 1: matrix
2 : imsd 1=MSD, 2=Preconditioned
0 : evaluate_eko_diff
0 : npdosao
0 0.0
2 : mvelsc
300.0D0 30.0D0 30 1.0D0 : tempw,tolp,nro...
500.0D0 8 15 1 : wnosep,nhc,nos...
5.0D-8 : frict
0 : mcnstr
DIST 1 3 1.83401
DIST 2 3 1.83401
BEND 1 3 2 104.23195
&ESM
BOUNDARY_CONDITION BARE
&END
In the current working directory, perform the following o...
- Combined system
$ mpirun -np 24 ./STATE < nfinp_1 > nfout_1
- Adsorbate
$ cd HFACH
$ mpirun -np 24 ./STATE < nfinp_1 > nfout_1
- Substrate
$ cd ../Ni
$ mpirun -np 24 ./STATE < nfinp_1 > nfout_1
** Prep of the COOP analysis [#ga0e82af]
After converging all the wave functions (./zaj.data, HFAC...
First, create a symbolic links in the current working dir...
$ ln -s HFACH/zaj.data zak1.data
$ ln -s Ni/zaj.data zak3.data
and then create a new input file for the preparation.
Let us copy nfinp_1 to nfinp_coop
$ cp nfinp_1 nfinp_coop
and change ICOND from 0 to 17 in nfinp_coop as
17 0 0 0 0 : icond, inipos, inivel, ininos, iniacc
Furthermore, we need to create 'nfcoop.data' to set the c...
'nfcoop.data' may look like:
2 : KSPIN
40 : KNV3
43 48 15 101 : NPDOSMO1 KPDOSMO1 KATM1 ...
0 0 0 0 : NPDOSMO2 KPDOSMO2 KATM2 ...
336 336 48 864 : NPDOSMO3 KPDOSMO3 KATM3 ...
-15.0 5.0 0.5 2001 : EMIN EMAX EWIDTH NPDOSE
Having prepared "nfcoop.data", execute STATE using nfinp_...
$ mpirun -np 24 ./STATE < nfinp_coop > nfout_coop
Finally, we need to prepare 'eko.data', a file containing...
$ state2eigen.pl nfout_1 > eko.data
** COOP analysis [#x19d8dda]
When all the preliminary calculations are successfully pe...
- coop.data
- coop_bij.data
- coop_sij.data
- eko.data
- nfcoop.data
and we are ready to perform COOP analysis!
Assuming the command search path for the COOP program ('c...
$ coop_analysis > coop.out
and densities of states (DOSs) projected onto the molecul...
To extract MOPDOSs, type
$ grep 'PDOS\:' coop.out | awk -F\: '{print $2}' > pdos....
To extract COOPs, type
$ grep 'COOP2\:' coop.out | awk -F\: '{print $2}' > coop...
In the current example, the system is spin polarized, and...
For convenience, we split them as follows:
$ wc -l pdos.dat
4006 pdos.dat
$ split -l 2003 pdos.dat; mv xaa pdos_up.dat; mv xab pdo...
$ wc -l coop2.dat
4006 coop2.dat
$ split -l 2003 coop2.dat; mv xaa coop2_up.dat; mv xab c...
Those files (pdos.dat/coop2.dat) contain energy and DOS d...
- 1st column: energy with respect to the Fermi level (in ...
- 2nd - NPDOSMO1 column (2nd - 1st MO, 3rd - 2nd MO, 4th ...
Then, spin-up MOPDOS for HOMO, LUMO, and LUMO+1 may be pl...
> plot 'pdos_up.dat' using ($1):($39) title 'HOMO ' wit...
'' using ($1):($40) title 'LUMO ' with...
'' using ($1):($41) title 'LUMO+1' with...
and spin-up COOP for HOMO (orbital #38), LUMO (orbital #3...
> plot 'coop2_up.dat' using ($1):($39) title 'HOMO ' wi...
'' using ($1):($40) title 'LUMO ' wi...
'' using ($1):($41) title 'LUMO+1' wi...
considering that HOMO is the 38th orbital in the current ...
** References [#t5c09734]
-R. Hoffmann, Rev. Mod. Phys. 60, 601 (1988).
-H. Aizawa and S. Tsuneyuki, Surf. Sci. 399, L364 (1998).
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