第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Oxygen molecule [#k112b541]
In this tutorial, how to perform calculation(s) of a mole...
#Contents
** Preliminary [#bc970db3]
In this tutorial, the O2 molecule is placed in a cubic bo...
The GBRV ultrasoft pseudopotential, kinetic energy cutoff...
** SCF calculation [#b9138eba]
*** Fixed moment calculation [#xe714aec]
We start with an SCF calculation using the following inpu...
-o2_scf.in
O2
O2 molecule in a box
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'o2'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 12
nosym = .true.
nspin = 2
tot_magnetization = 2.0
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
O 0.000000000000 0.000000000000 1.200000...
K_POINTS (gamma)
We also use a job script like following:
- o2.sh
#$ -S /bin/bash
#$ -cwd
#$ -q xe2.q
#$ -pe x12 12
#$ -N O2
#$ -o O2.out
#$ -e O2.err
#
module load intel/2020.2.254 intelmpi/2020.2.254
#
INPUT_FILE='o2_scf.in'
OUTPUT_FILE='o2_scf.out'
#
PW_DIR=/home/ikutaro/QE/src/qe-7.2/bin
#
MPI_COMMAND=mpirun
PW_COMMAND=pw.x
PW=$PW_DIR/$PW_COMMAND
#
I_MPI_PIN=1
I_MPI_FABRICS=shm:dapl
OMP_NUM_THREADS=1
#
$MPI_COMMAND $PW < $INPUT_FILE > $OUTPUT_FILE
To submit the job execute
$ qsub o2.sh
In this example, we perform the fixed moment calculation ...
tot_magnetization = 2.0
in the namelist &SYSTEM.
Note that nonzero initial magnetization should be given t...
starting_magnetization(1) = 0.5d0
When the convergence of the SCF calculation is achieved, ...
The total energy is the sum of the following terms:
one-electron contribution = -124.42909406 Ry
hartree contribution = 64.11909734 Ry
xc contribution = -14.24282541 Ry
ewald contribution = 10.24736697 Ry
total magnetization = 2.00 Bohr mag/cell
absolute magnetization = 2.05 Bohr mag/cell
and electron configuration as (by setting verbosity = 'hi...
------ SPIN UP ------------
k = 0.0000 0.0000 0.0000 ( 14336 PWs) bands ...
-32.8993 -20.2605 -13.4590 -13.4590 -13.4215 -6.5703...
0.8418 0.9710 0.9732 0.9749
occupation numbers
1.0000 1.0000 1.0000 1.0000 1.0000 1.0000...
0.0000 0.0000 0.0000 0.0000
------ SPIN DOWN ----------
k = 0.0000 0.0000 0.0000 ( 14336 PWs) bands ...
-31.7149 -18.4058 -12.4328 -11.5313 -11.5313 -4.1646...
1.0168 1.0686 1.0826 1.0826
occupation numbers
1.0000 1.0000 1.0000 1.0000 1.0000 0.0000...
0.0000 0.0000 0.0000 0.0000
highest occupied, lowest unoccupied level (ev): ...
*** Fixed occupation calculation [#ucd1be8e]
Alternatively, we can also perform calculations with fixe...
- o2_scf.in
O2
O2 molecule in a box
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'o2'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd =12
nosym = .true.
nspin = 2
occupations = 'from_input'
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
O 0.000000000000 0.000000000000 1.200000...
K_POINTS (gamma)
OCCUPATIONS
1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0
1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
The fixed moment calculation is enabled setting
occupations = 'from_input'
and
OCCUPATIONS
1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0
1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Note that the number of states (bands) should be consiste...
** Structural relaxation [#s024b02b]
Structural optimization can be performed by setting the c...
- o2_relax.in
O2
O2 molecule in a box
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'o2'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 12
nosym = .true.
nspin = 2
tot_magnetization = 2.0
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
O 0.000000000000 0.000000000000 1.200000...
K_POINTS (gamma)
To perform the structural relaxation
&ions
/
needs to be added in the input file.
In this example, the default force threshold (forc_conv_t...
** Calculation of the atomization energy [#f68e7f56]
Let us calculate the atomization energy, which is the ene...
\[
E_{\rm{a}} = E_{\rm{tot}}(\rm{O}_2) - 2 \times E_{\rm{tot...
\]
where $E_{\rm{tot}}(\rm{O}_2)$ and $E_{\rm{tot}}(\rm{O})$...
To perform the calculation of the spin polarized O atom i...
- o_scf.in
O
O atom in a box
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'o'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 1
ntyp = 1
nbnd = 8
nosym = .true.
nspin = 2
occupations = 'from_input'
one_atom_occupations = .true.
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.1
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
K_POINTS (gamma)
OCCUPATIONS
1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0
1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0
From my experience, it is better to use the fixed occupat...
one_atom_occupations = .true.
Furthermore, the SCF convergence of the atomic calculatio...
In this case, try to use small mixing_beta and increase e...
After the SCF convrgence, we can calculate the binding en...
Compare with the values in the literature, for example, H...
** Exercise [#dfacc88e]
The atomization energy, in particular the oxygen atom, is...
- different functional (RPBE, BEEF-vdW, for instance)
- different pseudo)potentials
-- Normconserving (O.pbe-mt.UPF, for instance)
-- PAW (O.pbe-n-kjpaw_psl.1.0.0.UPF, for instance))
and see the differences.~
It is also important to converge the results with respect...
終了行:
* Oxygen molecule [#k112b541]
In this tutorial, how to perform calculation(s) of a mole...
#Contents
** Preliminary [#bc970db3]
In this tutorial, the O2 molecule is placed in a cubic bo...
The GBRV ultrasoft pseudopotential, kinetic energy cutoff...
** SCF calculation [#b9138eba]
*** Fixed moment calculation [#xe714aec]
We start with an SCF calculation using the following inpu...
-o2_scf.in
O2
O2 molecule in a box
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'o2'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 12
nosym = .true.
nspin = 2
tot_magnetization = 2.0
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
O 0.000000000000 0.000000000000 1.200000...
K_POINTS (gamma)
We also use a job script like following:
- o2.sh
#$ -S /bin/bash
#$ -cwd
#$ -q xe2.q
#$ -pe x12 12
#$ -N O2
#$ -o O2.out
#$ -e O2.err
#
module load intel/2020.2.254 intelmpi/2020.2.254
#
INPUT_FILE='o2_scf.in'
OUTPUT_FILE='o2_scf.out'
#
PW_DIR=/home/ikutaro/QE/src/qe-7.2/bin
#
MPI_COMMAND=mpirun
PW_COMMAND=pw.x
PW=$PW_DIR/$PW_COMMAND
#
I_MPI_PIN=1
I_MPI_FABRICS=shm:dapl
OMP_NUM_THREADS=1
#
$MPI_COMMAND $PW < $INPUT_FILE > $OUTPUT_FILE
To submit the job execute
$ qsub o2.sh
In this example, we perform the fixed moment calculation ...
tot_magnetization = 2.0
in the namelist &SYSTEM.
Note that nonzero initial magnetization should be given t...
starting_magnetization(1) = 0.5d0
When the convergence of the SCF calculation is achieved, ...
The total energy is the sum of the following terms:
one-electron contribution = -124.42909406 Ry
hartree contribution = 64.11909734 Ry
xc contribution = -14.24282541 Ry
ewald contribution = 10.24736697 Ry
total magnetization = 2.00 Bohr mag/cell
absolute magnetization = 2.05 Bohr mag/cell
and electron configuration as (by setting verbosity = 'hi...
------ SPIN UP ------------
k = 0.0000 0.0000 0.0000 ( 14336 PWs) bands ...
-32.8993 -20.2605 -13.4590 -13.4590 -13.4215 -6.5703...
0.8418 0.9710 0.9732 0.9749
occupation numbers
1.0000 1.0000 1.0000 1.0000 1.0000 1.0000...
0.0000 0.0000 0.0000 0.0000
------ SPIN DOWN ----------
k = 0.0000 0.0000 0.0000 ( 14336 PWs) bands ...
-31.7149 -18.4058 -12.4328 -11.5313 -11.5313 -4.1646...
1.0168 1.0686 1.0826 1.0826
occupation numbers
1.0000 1.0000 1.0000 1.0000 1.0000 0.0000...
0.0000 0.0000 0.0000 0.0000
highest occupied, lowest unoccupied level (ev): ...
*** Fixed occupation calculation [#ucd1be8e]
Alternatively, we can also perform calculations with fixe...
- o2_scf.in
O2
O2 molecule in a box
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'o2'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd =12
nosym = .true.
nspin = 2
occupations = 'from_input'
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
O 0.000000000000 0.000000000000 1.200000...
K_POINTS (gamma)
OCCUPATIONS
1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0
1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
The fixed moment calculation is enabled setting
occupations = 'from_input'
and
OCCUPATIONS
1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0
1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Note that the number of states (bands) should be consiste...
** Structural relaxation [#s024b02b]
Structural optimization can be performed by setting the c...
- o2_relax.in
O2
O2 molecule in a box
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'o2'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 12
nosym = .true.
nspin = 2
tot_magnetization = 2.0
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
O 0.000000000000 0.000000000000 1.200000...
K_POINTS (gamma)
To perform the structural relaxation
&ions
/
needs to be added in the input file.
In this example, the default force threshold (forc_conv_t...
** Calculation of the atomization energy [#f68e7f56]
Let us calculate the atomization energy, which is the ene...
\[
E_{\rm{a}} = E_{\rm{tot}}(\rm{O}_2) - 2 \times E_{\rm{tot...
\]
where $E_{\rm{tot}}(\rm{O}_2)$ and $E_{\rm{tot}}(\rm{O})$...
To perform the calculation of the spin polarized O atom i...
- o_scf.in
O
O atom in a box
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'o'
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp/'
verbosity = 'high'
/
&system
ibrav = 1
A = 10.d0
nat = 1
ntyp = 1
nbnd = 8
nosym = .true.
nspin = 2
occupations = 'from_input'
one_atom_occupations = .true.
starting_magnetization(1) = 0.5d0
ecutwfc = 40.0
ecutrho = 320.0
/
&electrons
mixing_beta = 0.1
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
O 15.9994 o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
O 0.000000000000 0.000000000000 0.000000...
K_POINTS (gamma)
OCCUPATIONS
1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0
1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0
From my experience, it is better to use the fixed occupat...
one_atom_occupations = .true.
Furthermore, the SCF convergence of the atomic calculatio...
In this case, try to use small mixing_beta and increase e...
After the SCF convrgence, we can calculate the binding en...
Compare with the values in the literature, for example, H...
** Exercise [#dfacc88e]
The atomization energy, in particular the oxygen atom, is...
- different functional (RPBE, BEEF-vdW, for instance)
- different pseudo)potentials
-- Normconserving (O.pbe-mt.UPF, for instance)
-- PAW (O.pbe-n-kjpaw_psl.1.0.0.UPF, for instance))
and see the differences.~
It is also important to converge the results with respect...
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