第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Pyrite (FeS2) [#jeb2297a]
In this section, how to perform the electronic structure ...
** SCF calculation [#v9916338]
First of all, let us perform an SCF calculation using ''p...
Below is the input file used for the SCF calculation
- ''scf.in''
&CONTROL
calculation = 'scf'
etot_conv_thr = 1.2000000000d-04
forc_conv_thr = 1.0000000000d-04
outdir = './out/'
prefix = 'fes2'
pseudo_dir = '../pseudo/'
tprnfor = .true.
tstress = .true.
verbosity = 'high'
/
&SYSTEM
degauss = 2.0000000000d-02
ecutrho = 1.0800000000d+03
ecutwfc = 9.0000000000d+01
ibrav = 0
nat = 12
nosym = .false.
!nspin = 2
nbnd = 80
ntyp = 2
occupations = 'smearing'
smearing = 'cold'
!starting_magnetization(1) = 3.1250000000d-01
!starting_magnetization(2) = 1.0000000000d-01
/
&ELECTRONS
conv_thr = 2.4000000000d-09
electron_maxstep = 80
mixing_beta = 4.0000000000d-01
/
ATOMIC_SPECIES
Fe 55.845 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
S 32.065 s_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS crystal
Fe 0.0000000000 0.0000000000 0.000...
Fe 0.5000000000 0.0000000000 0.500...
Fe 0.0000000000 0.5000000000 0.500...
Fe 0.5000000000 0.5000000000 0.000...
S 0.3850400000 0.3850400000 0.385...
S 0.6149600000 0.6149600000 0.614...
S 0.1149600000 0.6149600000 0.885...
S 0.8850400000 0.3850400000 0.114...
S 0.6149600000 0.8850400000 0.114...
S 0.3850400000 0.1149600000 0.885...
S 0.8850400000 0.1149600000 0.614...
S 0.1149600000 0.8850400000 0.385...
K_POINTS automatic
4 4 4 0 0 0
CELL_PARAMETERS angstrom
5.4281000000 0.0000000000 0.0000000000
0.0000000000 5.4281000000 0.0000000000
0.0000000000 0.0000000000 5.4281000000
** Density of states calculation [#d2b48dcd]
After confirming the convergence of SCF, let us perform d...
Below is the input file for the DOS calculation.
- ''dos.in''
&DOS
outdir ='./out/'
prefix ='fes2'
fildos ='fes2.dos'
bz_sum = 'tetrahedra'
Emin = -85.0
Emax = 25.0
DeltaE = 0.01
/
In this exercise, the SCF calculation was performed with ...
** Refined Density of states calculation [#f83b2359]
To get more precise, let us perform a non-SCF (NSCF) calc...
This is not always necessary, but if necessary, perform a...
Remember this NSCF calculation can take longer than SCF c...
For this purpose set ''calculation'' ''nscf'' in the &CON...
calculation = 'nscf'
and finer k-point grid in the K_POINTS card, for example:
K_POINTS automatic
9 9 9 0 0 0
then the nscf calculation is done, perform the DOS calcul...
** Projected DOS calculation [#f5e17a06]
To get DOS projected onto the atomic orbitals (PDOS), let...
It is important to remember that unlike the DOS calculati...
Below is an input file for the PDOS calculation
- ''projwfc.in''
&PROJWFC
outdir = './out/'
prefix = 'fes2'
Emin = -25.00
Emax = 25.00
DeltaE = 0.01
/
For a better characterization of PDOS, it is useful to us...
This can be done by setting ''diag_basis'' .true. as
diag_basis = .true.
Furthermore, Lowdin population analysis is performed duri...
See the output file and search the word ''Lowdin Charges'...
Lowdin Charges:
Atom # 1: total charge = 16.8478, s = 2.4992,
Atom # 1: total charge = 16.8478, p = 7.3552, p...
Atom # 1: total charge = 16.8478, d = 6.9934, d...
Atom # 2: total charge = 16.8460, s = 2.4917,
Atom # 2: total charge = 16.8460, p = 7.3512, p...
Atom # 2: total charge = 16.8460, d = 7.0031, d...
Atom # 3: total charge = 16.8204, s = 2.4916,
Atom # 3: total charge = 16.8204, p = 7.3495, p...
Atom # 3: total charge = 16.8204, d = 6.9793, d...
Atom # 4: total charge = 16.8502, s = 2.4957,
Atom # 4: total charge = 16.8502, p = 7.3523, p...
Atom # 4: total charge = 16.8502, d = 7.0022, d...
Atom # 5: total charge = 5.4643, s = 1.4831,
Atom # 5: total charge = 5.4643, p = 3.9813, p...
Atom # 5: total charge = 5.4643, d = 0.0000, d...
Atom # 6: total charge = 5.4643, s = 1.4831,
Atom # 6: total charge = 5.4643, p = 3.9813, p...
Atom # 6: total charge = 5.4643, d = 0.0000, d...
Atom # 7: total charge = 5.4600, s = 1.4921,
Atom # 7: total charge = 5.4600, p = 3.9679, p...
Atom # 7: total charge = 5.4600, d = 0.0000, d...
Atom # 8: total charge = 5.4600, s = 1.4921,
Atom # 8: total charge = 5.4600, p = 3.9679, p...
Atom # 8: total charge = 5.4600, d = 0.0000, d...
Atom # 9: total charge = 5.4591, s = 1.4921,
Atom # 9: total charge = 5.4591, p = 3.9670, p...
Atom # 9: total charge = 5.4591, d = 0.0000, d...
Atom # 10: total charge = 5.4591, s = 1.4921,
Atom # 10: total charge = 5.4591, p = 3.9670, p...
Atom # 10: total charge = 5.4591, d = 0.0000, d...
Atom # 11: total charge = 5.4606, s = 1.4873,
Atom # 11: total charge = 5.4606, p = 3.9732, p...
Atom # 11: total charge = 5.4606, d = 0.0000, d...
Atom # 12: total charge = 5.4606, s = 1.4873,
Atom # 12: total charge = 5.4606, p = 3.9732, p...
Atom # 12: total charge = 5.4606, d = 0.0000, d...
Spilling Parameter: 0.0085
This may be helpful to get an insight into the charge (st...
** Bader charge analysis [#lde073e7]
To further gain an insight into the charge state/atomic c...
*** Preparation [#h9f6de65]
To perform the Bader charge analysis, the charge density ...
To do this, one needs to use ''pp.x''.
Below is an example for ''pp.x'' to generate a charge den...
- ''pp.in''
&INPUTPP
prefix = 'fes2'
outdir = './out/'
filplot = 'fes2'
plot_num = 0
/
&PLOT
iflag = 3
output_format = 6
fileout = 'fes2_val.cube'
/
''plot_num'' is used to output the charge density in real...
*** Execution [#u4b77208]
Supposing the path to the program ''bader'' is set, one c...
bader fes2_val.cube
Output may look like:
GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)
OPEN ... fes2_val.cube
GAUSSIAN-STYLE INPUT FILE
DENSITY-GRID: 108 x 108 x 108
CLOSE ... fes2_val.cube
RUN TIME: 0.27 SECONDS
CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: **********************
REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 428375
REASSIGNED POINTS: 28371
RUN TIME: 2.29 SECONDS
CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 0.22 SECONDS
WRITING BADER ATOMIC CHARGES TO ACF.dat
WRITING BADER VOLUME CHARGES TO BCF.dat
NUMBER OF BADER MAXIMA FOUND: 72
SIGNIFICANT MAXIMA FOUND: 72
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 112.00003
The calculated Bader charges are written to ''ACF.dat'' as
# X Y Z CHARGE ...
-------------------------------------------------------...
1 10.257622 10.257622 10.257622 15.308219 ...
2 5.128811 10.257622 5.128811 15.308219 ...
3 10.257622 5.128811 5.128811 15.308219 ...
4 5.128811 5.128811 10.257622 15.308219 ...
5 3.949595 3.949595 3.949595 6.354199 ...
6 6.308027 6.308027 6.308027 6.337589 ...
7 1.179216 6.308027 9.078406 6.337589 ...
8 9.078406 3.949595 1.179216 6.354199 ...
9 6.308027 9.078406 1.179216 6.337589 ...
10 3.949595 1.179216 9.078406 6.354199 ...
11 9.078406 1.179216 6.308027 6.354199 ...
12 1.179216 9.078406 3.949595 6.337589 ...
-------------------------------------------------------...
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 112.0000
Note the charge is based on the valence charge defined by...
In this example, we use the following pseudopotentials:
- ''Fe.pbe-spn-kjpaw_psl.0.2.1.UPF''
- ''s_pbe_v1.4.uspp.F.UPF''
More specifically, the respective valence configurations ...
- ''Fe.pbe-spn-kjpaw_psl.0.2.1.UPF''
nl pn l occ Rcut Rcut US E pseu
3S 1 0 2.00 1.100 1.300 -6.910119
4S 2 0 2.00 0.800 1.400 -0.388933
3P 2 1 6.00 1.000 1.300 -4.413015
4P 3 1 0.00 1.000 1.600 -0.097407
3D 3 2 6.00 1.400 2.000 -0.551558
- ''s_pbe_v1.4.uspp.F.UPF''
nl pn l occ Rcut Rcut US...
3S 3 0 2.00 0.00000000000 1.50000000000...
3P 3 1 4.00 0.00000000000 1.50000000000...
It can be seen that the numbers of valence electros for F...
Based on simple mathematics, it seems Fe is positively ch...
Compare with the Lowdin charges.
For more precise discussion on the actual charge state, o...
終了行:
* Pyrite (FeS2) [#jeb2297a]
In this section, how to perform the electronic structure ...
** SCF calculation [#v9916338]
First of all, let us perform an SCF calculation using ''p...
Below is the input file used for the SCF calculation
- ''scf.in''
&CONTROL
calculation = 'scf'
etot_conv_thr = 1.2000000000d-04
forc_conv_thr = 1.0000000000d-04
outdir = './out/'
prefix = 'fes2'
pseudo_dir = '../pseudo/'
tprnfor = .true.
tstress = .true.
verbosity = 'high'
/
&SYSTEM
degauss = 2.0000000000d-02
ecutrho = 1.0800000000d+03
ecutwfc = 9.0000000000d+01
ibrav = 0
nat = 12
nosym = .false.
!nspin = 2
nbnd = 80
ntyp = 2
occupations = 'smearing'
smearing = 'cold'
!starting_magnetization(1) = 3.1250000000d-01
!starting_magnetization(2) = 1.0000000000d-01
/
&ELECTRONS
conv_thr = 2.4000000000d-09
electron_maxstep = 80
mixing_beta = 4.0000000000d-01
/
ATOMIC_SPECIES
Fe 55.845 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
S 32.065 s_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS crystal
Fe 0.0000000000 0.0000000000 0.000...
Fe 0.5000000000 0.0000000000 0.500...
Fe 0.0000000000 0.5000000000 0.500...
Fe 0.5000000000 0.5000000000 0.000...
S 0.3850400000 0.3850400000 0.385...
S 0.6149600000 0.6149600000 0.614...
S 0.1149600000 0.6149600000 0.885...
S 0.8850400000 0.3850400000 0.114...
S 0.6149600000 0.8850400000 0.114...
S 0.3850400000 0.1149600000 0.885...
S 0.8850400000 0.1149600000 0.614...
S 0.1149600000 0.8850400000 0.385...
K_POINTS automatic
4 4 4 0 0 0
CELL_PARAMETERS angstrom
5.4281000000 0.0000000000 0.0000000000
0.0000000000 5.4281000000 0.0000000000
0.0000000000 0.0000000000 5.4281000000
** Density of states calculation [#d2b48dcd]
After confirming the convergence of SCF, let us perform d...
Below is the input file for the DOS calculation.
- ''dos.in''
&DOS
outdir ='./out/'
prefix ='fes2'
fildos ='fes2.dos'
bz_sum = 'tetrahedra'
Emin = -85.0
Emax = 25.0
DeltaE = 0.01
/
In this exercise, the SCF calculation was performed with ...
** Refined Density of states calculation [#f83b2359]
To get more precise, let us perform a non-SCF (NSCF) calc...
This is not always necessary, but if necessary, perform a...
Remember this NSCF calculation can take longer than SCF c...
For this purpose set ''calculation'' ''nscf'' in the &CON...
calculation = 'nscf'
and finer k-point grid in the K_POINTS card, for example:
K_POINTS automatic
9 9 9 0 0 0
then the nscf calculation is done, perform the DOS calcul...
** Projected DOS calculation [#f5e17a06]
To get DOS projected onto the atomic orbitals (PDOS), let...
It is important to remember that unlike the DOS calculati...
Below is an input file for the PDOS calculation
- ''projwfc.in''
&PROJWFC
outdir = './out/'
prefix = 'fes2'
Emin = -25.00
Emax = 25.00
DeltaE = 0.01
/
For a better characterization of PDOS, it is useful to us...
This can be done by setting ''diag_basis'' .true. as
diag_basis = .true.
Furthermore, Lowdin population analysis is performed duri...
See the output file and search the word ''Lowdin Charges'...
Lowdin Charges:
Atom # 1: total charge = 16.8478, s = 2.4992,
Atom # 1: total charge = 16.8478, p = 7.3552, p...
Atom # 1: total charge = 16.8478, d = 6.9934, d...
Atom # 2: total charge = 16.8460, s = 2.4917,
Atom # 2: total charge = 16.8460, p = 7.3512, p...
Atom # 2: total charge = 16.8460, d = 7.0031, d...
Atom # 3: total charge = 16.8204, s = 2.4916,
Atom # 3: total charge = 16.8204, p = 7.3495, p...
Atom # 3: total charge = 16.8204, d = 6.9793, d...
Atom # 4: total charge = 16.8502, s = 2.4957,
Atom # 4: total charge = 16.8502, p = 7.3523, p...
Atom # 4: total charge = 16.8502, d = 7.0022, d...
Atom # 5: total charge = 5.4643, s = 1.4831,
Atom # 5: total charge = 5.4643, p = 3.9813, p...
Atom # 5: total charge = 5.4643, d = 0.0000, d...
Atom # 6: total charge = 5.4643, s = 1.4831,
Atom # 6: total charge = 5.4643, p = 3.9813, p...
Atom # 6: total charge = 5.4643, d = 0.0000, d...
Atom # 7: total charge = 5.4600, s = 1.4921,
Atom # 7: total charge = 5.4600, p = 3.9679, p...
Atom # 7: total charge = 5.4600, d = 0.0000, d...
Atom # 8: total charge = 5.4600, s = 1.4921,
Atom # 8: total charge = 5.4600, p = 3.9679, p...
Atom # 8: total charge = 5.4600, d = 0.0000, d...
Atom # 9: total charge = 5.4591, s = 1.4921,
Atom # 9: total charge = 5.4591, p = 3.9670, p...
Atom # 9: total charge = 5.4591, d = 0.0000, d...
Atom # 10: total charge = 5.4591, s = 1.4921,
Atom # 10: total charge = 5.4591, p = 3.9670, p...
Atom # 10: total charge = 5.4591, d = 0.0000, d...
Atom # 11: total charge = 5.4606, s = 1.4873,
Atom # 11: total charge = 5.4606, p = 3.9732, p...
Atom # 11: total charge = 5.4606, d = 0.0000, d...
Atom # 12: total charge = 5.4606, s = 1.4873,
Atom # 12: total charge = 5.4606, p = 3.9732, p...
Atom # 12: total charge = 5.4606, d = 0.0000, d...
Spilling Parameter: 0.0085
This may be helpful to get an insight into the charge (st...
** Bader charge analysis [#lde073e7]
To further gain an insight into the charge state/atomic c...
*** Preparation [#h9f6de65]
To perform the Bader charge analysis, the charge density ...
To do this, one needs to use ''pp.x''.
Below is an example for ''pp.x'' to generate a charge den...
- ''pp.in''
&INPUTPP
prefix = 'fes2'
outdir = './out/'
filplot = 'fes2'
plot_num = 0
/
&PLOT
iflag = 3
output_format = 6
fileout = 'fes2_val.cube'
/
''plot_num'' is used to output the charge density in real...
*** Execution [#u4b77208]
Supposing the path to the program ''bader'' is set, one c...
bader fes2_val.cube
Output may look like:
GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)
OPEN ... fes2_val.cube
GAUSSIAN-STYLE INPUT FILE
DENSITY-GRID: 108 x 108 x 108
CLOSE ... fes2_val.cube
RUN TIME: 0.27 SECONDS
CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: **********************
REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 428375
REASSIGNED POINTS: 28371
RUN TIME: 2.29 SECONDS
CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 0.22 SECONDS
WRITING BADER ATOMIC CHARGES TO ACF.dat
WRITING BADER VOLUME CHARGES TO BCF.dat
NUMBER OF BADER MAXIMA FOUND: 72
SIGNIFICANT MAXIMA FOUND: 72
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 112.00003
The calculated Bader charges are written to ''ACF.dat'' as
# X Y Z CHARGE ...
-------------------------------------------------------...
1 10.257622 10.257622 10.257622 15.308219 ...
2 5.128811 10.257622 5.128811 15.308219 ...
3 10.257622 5.128811 5.128811 15.308219 ...
4 5.128811 5.128811 10.257622 15.308219 ...
5 3.949595 3.949595 3.949595 6.354199 ...
6 6.308027 6.308027 6.308027 6.337589 ...
7 1.179216 6.308027 9.078406 6.337589 ...
8 9.078406 3.949595 1.179216 6.354199 ...
9 6.308027 9.078406 1.179216 6.337589 ...
10 3.949595 1.179216 9.078406 6.354199 ...
11 9.078406 1.179216 6.308027 6.354199 ...
12 1.179216 9.078406 3.949595 6.337589 ...
-------------------------------------------------------...
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 112.0000
Note the charge is based on the valence charge defined by...
In this example, we use the following pseudopotentials:
- ''Fe.pbe-spn-kjpaw_psl.0.2.1.UPF''
- ''s_pbe_v1.4.uspp.F.UPF''
More specifically, the respective valence configurations ...
- ''Fe.pbe-spn-kjpaw_psl.0.2.1.UPF''
nl pn l occ Rcut Rcut US E pseu
3S 1 0 2.00 1.100 1.300 -6.910119
4S 2 0 2.00 0.800 1.400 -0.388933
3P 2 1 6.00 1.000 1.300 -4.413015
4P 3 1 0.00 1.000 1.600 -0.097407
3D 3 2 6.00 1.400 2.000 -0.551558
- ''s_pbe_v1.4.uspp.F.UPF''
nl pn l occ Rcut Rcut US...
3S 3 0 2.00 0.00000000000 1.50000000000...
3P 3 1 4.00 0.00000000000 1.50000000000...
It can be seen that the numbers of valence electros for F...
Based on simple mathematics, it seems Fe is positively ch...
Compare with the Lowdin charges.
For more precise discussion on the actual charge state, o...
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