第一原理分子動力学プログラム STATE Senri Wiki
開始行:
*Crystalline Al [#jb02f7c9]
In this example, how to determine the equilibrium lattice...
Since the stress is not yet implemented in the official v...
** Cell optimization [#w76c80cd]
- Job script (qsub_seq.sh)~
Here, instead of creating input files one by one, let us ...
#$ -S /bin/sh
#$ -cwd
#$ -pe fillup 6
#$ -N Al
#disable OPENMP parallelism
export OMP_NUM_THREADS=1
# execuable of the STATE code
ln -fs ${HOME}/STATE/src/STATE .
# pseudopotential data
ln -fs ${HOME}/STATE/gncpp/pot.Al_pbe1 fort.37
# launch STATE
for a in $(seq 7.50 0.10 7.90)
do
INPUT_FILE=nfinp_a${a}
OUTPUT_FILE=nfout_a${a}
cat > ${INPUT_FILE} << EOF
0 0 0 0 0 0 : I_CTRL(1:6) (DUMMY)
4.00 8.00 1 1 1 : GMAX GMAXP NTYP N...
221 2 : NUM_SPACE_GROUP T...
${a} ${a} ${a} 90.00 90.00 90.00 : A B C ALPHA BETA ...
12 12 12 1 1 1 : K_MESH
0 0 : NCORD NINV : IWEI...
0.00 0.00 0.00 1 0 1 : POS(1:3) IWEI IMD...
13 0.50 26.98 6 1 0.20 : IATOMN ALFA AMION...
0 0 0 0 0 : ICOND INIPOS INIV...
0 1 : IPRE IPRI
30 30 0 84200.00 0 : NMD1 NMD2 LAST_IT...
6 1 : WAY_MIX MIX_WHAT
0 20 0.60 : ITER_START KBXMIX...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTIM3...
300.00 4 1 0.50D-09 : DTIO IMDALG IEXPL...
-0.0020 0.50D+03 0 : WIDTH FORCCR ISTR...
ggapbe 1 : XCTYPE KSPIN
2.00 : DESTM
101 : NBZTYP
4 4 4 : DUMMY
4 4 4 : DUMMY
6 : KEG
1 : NEXTST
0 : DUMMY
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.00 : SM_N DOPPING
EOF
mpirun -np $NSLOTS ./STATE < ${INPUT_FILE} > ${OUTPUT_FI...
done
After the calculations, let us use "getetot.sh" placed in...
7.5 -2.07149508
7.6 -2.07210987
7.7 -2.07223992
7.8 -2.07193773
7.9 -2.07125357
Use gnuplot or whatever software to fit the total energy ...
** Band strucure calculation [#rb127cad]
To perform the band structure calculation, we need to a S...
- Input file for SCF (nfinp_dav)
0 0 0 0 0 0 : I_CTRL(1:6) (DU...
4.00 8.00 1 1 1 : GMAX GMAXP NTYP...
221 2 : NUM_SPACE_GROUP...
7.60 7.60 7.60 90.00 90.00 90.00 : A B C ALPHA BET...
06 06 06 1 1 1 : N1 N2 N3 M1 M2 M3
0 0 : NCORD, NINV
0.00 0.00 0.00 1 0 1 : CPS(1,1:3) IWEI...
13 0.50 26.98 6 1 0.2 : IATOMN ALFA AMI...
0 0 0 0 0 : ICOND INIPOS IN...
0 1 : IPRE IPRI
30 30 0 84200.00 0 : NMD1 NMD2 LAST_...
6 1 : WAY_MIX MIX_WHAT
0 20 0.60 : ITER_START KBXM...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTI...
300.00 4 1 0.50D-09 : DTIO IMDALG IEX...
-0.002 0 0.50D+03 0 : WIDTH FORCCR IS...
ggapbe 1 : XCTYPE KSPIN
2.00 : DESTM
101 : NBZTYPE
4 4 4 : NKX NKY NKZ (DU...
4 4 4 : NKX2 NKY2 NKZ2 ...
6 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.000 : SM_N DOPPING (D...
- Input file for the band structure calculation (nfinp_ba...
0 0 0 0 0 0 : I_CTRL(1:6) (DU...
4.00 8.00 1 1 1 : GMAX GMAXP NTYP...
221 2 : NUM_SPACE_GROUP...
7.60 7.60 7.60 90.00 90.00 90.00 : A B C ALPHA BET...
06 06 06 1 1 1 : N1 N2 N3 M1 M2 M3
0 0 : NCORD, NINV
0.00 0.00 0.00 1 0 1 : CPS(1,1:3) IWEI...
13 0.50 26.98 6 1 0.2 : IATOMN ALFA AMI...
22 0 0 0 0 : ICOND INIPOS IN...
0 1 : IPRE IPRI
30 30 0 84200.00 0 : NMD1 NMD2 LAST_...
6 1 : WAY_MIX MIX_WHAT
0 20 0.60 : ITER_START KBXM...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTI...
300.00 4 1 0.50D-09 : DTIO IMDALG IEX...
-0.0020 0.50D+03 0 : WIDTH FORCCR IS...
ggapbe 1 : XCTYPE KSPIN
2.00 : DESTM
101 : NBZTYPE
4 4 4 : NKX NKY NKZ (DU...
4 4 4 : NKX2 NKY2 NKZ2 ...
6 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.000 : SM_N DOPPING (D...
&KPOINTS_BAND
NKSEG 4
KMESH 40 20 20 20
KPOINTS
0.000 0.000 0.000
0.000 0.500 0.500
0.250 0.500 0.750
0.500 0.500 0.500
0.000 0.000 0.000
&END
In the band structure calculation, we set ICOND=22.
In addtion, high symmetry points and lines should be spec...
This can be done by adding the section &KPOINTS_BAND ... ...
Here NKSEG is the number of k-point segment (and the numb...
When the band structure calculation converges, "energy.da...
To plot the band structure with gnuplot or xmgrace, I use...
The number of bands and k-points are extracted in the ban...
Below, a gnuplot script to plot the band structure is sho...
G=0.00000000
X=0.82673491
W=1.24010236
L=1.82469222
G2=2.54066566
emin=-12.25
emax=4.25
xmin=0.0
xmax=G2
set xrange [xmin:xmax]
set yrange [emin:emax]
set arrow from G,emin to G,emax nohead lt 0
set arrow from X,emin to X,emax nohead lt 0
set arrow from W,emin to W,emax nohead lt 0
set arrow from L,emin to L,emax nohead lt 0
set arrow from G2,emin to G2,emax nohead lt 0
set xzeroaxis lt 0
unset xtics
set ylabel 'Energy (eV)'
plot 'band.data' with points pt 7 ps 2
pause -1
Type
$ gnuplot band.gp
to view the band structure.
終了行:
*Crystalline Al [#jb02f7c9]
In this example, how to determine the equilibrium lattice...
Since the stress is not yet implemented in the official v...
** Cell optimization [#w76c80cd]
- Job script (qsub_seq.sh)~
Here, instead of creating input files one by one, let us ...
#$ -S /bin/sh
#$ -cwd
#$ -pe fillup 6
#$ -N Al
#disable OPENMP parallelism
export OMP_NUM_THREADS=1
# execuable of the STATE code
ln -fs ${HOME}/STATE/src/STATE .
# pseudopotential data
ln -fs ${HOME}/STATE/gncpp/pot.Al_pbe1 fort.37
# launch STATE
for a in $(seq 7.50 0.10 7.90)
do
INPUT_FILE=nfinp_a${a}
OUTPUT_FILE=nfout_a${a}
cat > ${INPUT_FILE} << EOF
0 0 0 0 0 0 : I_CTRL(1:6) (DUMMY)
4.00 8.00 1 1 1 : GMAX GMAXP NTYP N...
221 2 : NUM_SPACE_GROUP T...
${a} ${a} ${a} 90.00 90.00 90.00 : A B C ALPHA BETA ...
12 12 12 1 1 1 : K_MESH
0 0 : NCORD NINV : IWEI...
0.00 0.00 0.00 1 0 1 : POS(1:3) IWEI IMD...
13 0.50 26.98 6 1 0.20 : IATOMN ALFA AMION...
0 0 0 0 0 : ICOND INIPOS INIV...
0 1 : IPRE IPRI
30 30 0 84200.00 0 : NMD1 NMD2 LAST_IT...
6 1 : WAY_MIX MIX_WHAT
0 20 0.60 : ITER_START KBXMIX...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTIM3...
300.00 4 1 0.50D-09 : DTIO IMDALG IEXPL...
-0.0020 0.50D+03 0 : WIDTH FORCCR ISTR...
ggapbe 1 : XCTYPE KSPIN
2.00 : DESTM
101 : NBZTYP
4 4 4 : DUMMY
4 4 4 : DUMMY
6 : KEG
1 : NEXTST
0 : DUMMY
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.00 : SM_N DOPPING
EOF
mpirun -np $NSLOTS ./STATE < ${INPUT_FILE} > ${OUTPUT_FI...
done
After the calculations, let us use "getetot.sh" placed in...
7.5 -2.07149508
7.6 -2.07210987
7.7 -2.07223992
7.8 -2.07193773
7.9 -2.07125357
Use gnuplot or whatever software to fit the total energy ...
** Band strucure calculation [#rb127cad]
To perform the band structure calculation, we need to a S...
- Input file for SCF (nfinp_dav)
0 0 0 0 0 0 : I_CTRL(1:6) (DU...
4.00 8.00 1 1 1 : GMAX GMAXP NTYP...
221 2 : NUM_SPACE_GROUP...
7.60 7.60 7.60 90.00 90.00 90.00 : A B C ALPHA BET...
06 06 06 1 1 1 : N1 N2 N3 M1 M2 M3
0 0 : NCORD, NINV
0.00 0.00 0.00 1 0 1 : CPS(1,1:3) IWEI...
13 0.50 26.98 6 1 0.2 : IATOMN ALFA AMI...
0 0 0 0 0 : ICOND INIPOS IN...
0 1 : IPRE IPRI
30 30 0 84200.00 0 : NMD1 NMD2 LAST_...
6 1 : WAY_MIX MIX_WHAT
0 20 0.60 : ITER_START KBXM...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTI...
300.00 4 1 0.50D-09 : DTIO IMDALG IEX...
-0.002 0 0.50D+03 0 : WIDTH FORCCR IS...
ggapbe 1 : XCTYPE KSPIN
2.00 : DESTM
101 : NBZTYPE
4 4 4 : NKX NKY NKZ (DU...
4 4 4 : NKX2 NKY2 NKZ2 ...
6 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.000 : SM_N DOPPING (D...
- Input file for the band structure calculation (nfinp_ba...
0 0 0 0 0 0 : I_CTRL(1:6) (DU...
4.00 8.00 1 1 1 : GMAX GMAXP NTYP...
221 2 : NUM_SPACE_GROUP...
7.60 7.60 7.60 90.00 90.00 90.00 : A B C ALPHA BET...
06 06 06 1 1 1 : N1 N2 N3 M1 M2 M3
0 0 : NCORD, NINV
0.00 0.00 0.00 1 0 1 : CPS(1,1:3) IWEI...
13 0.50 26.98 6 1 0.2 : IATOMN ALFA AMI...
22 0 0 0 0 : ICOND INIPOS IN...
0 1 : IPRE IPRI
30 30 0 84200.00 0 : NMD1 NMD2 LAST_...
6 1 : WAY_MIX MIX_WHAT
0 20 0.60 : ITER_START KBXM...
0.20 0.30 0.20 0.20 0.20 : DTIM1 DTIM2 DTI...
300.00 4 1 0.50D-09 : DTIO IMDALG IEX...
-0.0020 0.50D+03 0 : WIDTH FORCCR IS...
ggapbe 1 : XCTYPE KSPIN
2.00 : DESTM
101 : NBZTYPE
4 4 4 : NKX NKY NKZ (DU...
4 4 4 : NKX2 NKY2 NKZ2 ...
6 : KEG
1 : NEXTST
0 : (DUMMY)
2 : IMSD
0 : EVALUATE_EKO_DIFF
0 : NPDOSAO
0 0.000 : SM_N DOPPING (D...
&KPOINTS_BAND
NKSEG 4
KMESH 40 20 20 20
KPOINTS
0.000 0.000 0.000
0.000 0.500 0.500
0.250 0.500 0.750
0.500 0.500 0.500
0.000 0.000 0.000
&END
In the band structure calculation, we set ICOND=22.
In addtion, high symmetry points and lines should be spec...
This can be done by adding the section &KPOINTS_BAND ... ...
Here NKSEG is the number of k-point segment (and the numb...
When the band structure calculation converges, "energy.da...
To plot the band structure with gnuplot or xmgrace, I use...
The number of bands and k-points are extracted in the ban...
Below, a gnuplot script to plot the band structure is sho...
G=0.00000000
X=0.82673491
W=1.24010236
L=1.82469222
G2=2.54066566
emin=-12.25
emax=4.25
xmin=0.0
xmax=G2
set xrange [xmin:xmax]
set yrange [emin:emax]
set arrow from G,emin to G,emax nohead lt 0
set arrow from X,emin to X,emax nohead lt 0
set arrow from W,emin to W,emax nohead lt 0
set arrow from L,emin to L,emax nohead lt 0
set arrow from G2,emin to G2,emax nohead lt 0
set xzeroaxis lt 0
unset xtics
set ylabel 'Energy (eV)'
plot 'band.data' with points pt 7 ps 2
pause -1
Type
$ gnuplot band.gp
to view the band structure.
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