第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Vibrational mode analysis of a hydrogen molecule [#g740...
In this tutorial, how to calculate vibrational frequencie...
#Contents
** Preliminary [#wee17bda]
in the parent directory build ph.x, if not, by typing
$ make ph
** Geometry optimization [#b7ee314a]
To calculate vibrational frequencies accurately, we shoul...
Here the molecule is put in a cubic box with the cell edg...
&control
calculation = 'relax'
restart_mode = 'from_scratch',
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp'
prefix = 'h2'
tprnfor = .true.
forc_conv_thr = 1.d-4
/
&system
ibrav = 1
A = 15.d0
nat = 2
ntyp = 1
ecutwfc = 50.0
ecutrho = 400.0
nbnd = 8
/
&electrons
diagonalization='david'
conv_thr = 1.0e-12
mixing_beta = 0.7
/
&ions
/
ATOMIC_SPECIES
H 1.00794 h_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
H 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 0.75000000
K_POINTS (gamma)
Then execute pw.x by executing the following (and/or alik...
$ mpirun -np 2 $HOME/QE/src/qe-6.2.1/bin/pw.x < h2_relax...
** SCF calculation [#n46ac2a2]
We then perform a single-shot SCF calculation by using th...
For this purpose, I recommend using a very tight converge...
Following is an example of the input file.
&control
calculation = 'scf'
restart_mode = 'from_scratch',
pseudo_dir = '/home/k0227/k022700/QE/pseudo'
outdir = './tmp'
prefix = 'h2'
tprnfor = .true.
/
&system
ibrav = 1
A = 15.d0
nat = 2
ntyp = 1
ecutwfc = 50.0
ecutrho = 400.0
nbnd = 8
/
&electrons
diagonalization='david'
conv_thr = 1.0e-14
mixing_beta = 0.7
/
ATOMIC_SPECIES
H 1.00794 h_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
H 0.000000000 0.000000000 -0.005787349
H 0.000000000 0.000000000 0.755787349
K_POINTS (automatic)
1 1 1 0 0 0
Note that ph.x is NOT able to read real wave functions ob...
K_POINTS (automatic)
1 1 1 0 0 0
"phcg.x" may be able to handle real wave functions, but t...
Execute pw.x by executing the following (and/or alike):
$ mpirun -np 2 $HOME/QE/src/qe-6.2.1/bin/pw.x < h2_scf.i...
** Vibrational mode analysis [#sb70522f]
Having obtained the optimized geometry and the unperturbe...
Below is an (minimal) input file for the ph.x program.
H2 molecule
&inputph
outdir = './tmp'
prefix = 'h2'
fildyn = 'h2.dyn'
epsil = .true.
tr2_ph = 1.d-18
!recover = .true.
/
0.0 0.0 0.0
Here "outdir" and "prefix" should be the same as those in...
"fildyn" is the name of file, in which dynamical matrix i...
"epsil" allows one to compute the dielectric matrix.
Convergence threshold "tr2_ph" should be as tight as 1.e-...
With "recover = .true.", one is able to restart the vibra...
For a gas-phase molecule, only the gamma-point is needed ...
To do this, the q-point (0.0 0.0 0.0) is explicitly speci...
To run ph.x the following command is executed
$ mpirun -np 2 $HOME/QE/src/qe-6.4.1/bin/ph.x < h2_ph.in...
and one get the vibrational frequencies in the output fil...
Diagonalizing the dynamical matrix
q = ( 0.000000000 0.000000000 0.000000000 )
*******************************************************...
freq ( 1) = -3.582291 [THz] = -119.49237...
freq ( 2) = -3.582290 [THz] = -119.49234...
freq ( 3) = -3.552544 [THz] = -118.50012...
freq ( 4) = -3.552544 [THz] = -118.50011...
freq ( 5) = -2.974216 [THz] = -99.20917...
freq ( 6) = 131.121910 [THz] = 4373.75613...
*******************************************************...
Negative frequency indicates the imaginary mode. Note tha...
In addition, by using the "dynmat.x" program, vibrational...
The following is the minimalist input file (dynmat.in):
&input
fildyn='h2.dyn'
filout='dynmat.out'
/
By executing the following
$ $HOME/QE/src/qe-6.4.1/bin/dynmat.x < dynmat.in > dynma...
we obtain "dynmat.axsf","dynmat.mold", in which vibration...
When XCrySDen is not available, copy ~ikutaro/QE/tools/ax...
$ cp ~ikutaro/QE/tools/axsf2xsf.sh .
and execute
$ ./axsf2xsf.sh dynmat.axsf
then we get dynmat_#*.xsf for each mode. These file can b...
終了行:
* Vibrational mode analysis of a hydrogen molecule [#g740...
In this tutorial, how to calculate vibrational frequencie...
#Contents
** Preliminary [#wee17bda]
in the parent directory build ph.x, if not, by typing
$ make ph
** Geometry optimization [#b7ee314a]
To calculate vibrational frequencies accurately, we shoul...
Here the molecule is put in a cubic box with the cell edg...
&control
calculation = 'relax'
restart_mode = 'from_scratch',
pseudo_dir = '/home/ikutaro/QE/pseudo'
outdir = './tmp'
prefix = 'h2'
tprnfor = .true.
forc_conv_thr = 1.d-4
/
&system
ibrav = 1
A = 15.d0
nat = 2
ntyp = 1
ecutwfc = 50.0
ecutrho = 400.0
nbnd = 8
/
&electrons
diagonalization='david'
conv_thr = 1.0e-12
mixing_beta = 0.7
/
&ions
/
ATOMIC_SPECIES
H 1.00794 h_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
H 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 0.75000000
K_POINTS (gamma)
Then execute pw.x by executing the following (and/or alik...
$ mpirun -np 2 $HOME/QE/src/qe-6.2.1/bin/pw.x < h2_relax...
** SCF calculation [#n46ac2a2]
We then perform a single-shot SCF calculation by using th...
For this purpose, I recommend using a very tight converge...
Following is an example of the input file.
&control
calculation = 'scf'
restart_mode = 'from_scratch',
pseudo_dir = '/home/k0227/k022700/QE/pseudo'
outdir = './tmp'
prefix = 'h2'
tprnfor = .true.
/
&system
ibrav = 1
A = 15.d0
nat = 2
ntyp = 1
ecutwfc = 50.0
ecutrho = 400.0
nbnd = 8
/
&electrons
diagonalization='david'
conv_thr = 1.0e-14
mixing_beta = 0.7
/
ATOMIC_SPECIES
H 1.00794 h_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS (angstrom)
H 0.000000000 0.000000000 -0.005787349
H 0.000000000 0.000000000 0.755787349
K_POINTS (automatic)
1 1 1 0 0 0
Note that ph.x is NOT able to read real wave functions ob...
K_POINTS (automatic)
1 1 1 0 0 0
"phcg.x" may be able to handle real wave functions, but t...
Execute pw.x by executing the following (and/or alike):
$ mpirun -np 2 $HOME/QE/src/qe-6.2.1/bin/pw.x < h2_scf.i...
** Vibrational mode analysis [#sb70522f]
Having obtained the optimized geometry and the unperturbe...
Below is an (minimal) input file for the ph.x program.
H2 molecule
&inputph
outdir = './tmp'
prefix = 'h2'
fildyn = 'h2.dyn'
epsil = .true.
tr2_ph = 1.d-18
!recover = .true.
/
0.0 0.0 0.0
Here "outdir" and "prefix" should be the same as those in...
"fildyn" is the name of file, in which dynamical matrix i...
"epsil" allows one to compute the dielectric matrix.
Convergence threshold "tr2_ph" should be as tight as 1.e-...
With "recover = .true.", one is able to restart the vibra...
For a gas-phase molecule, only the gamma-point is needed ...
To do this, the q-point (0.0 0.0 0.0) is explicitly speci...
To run ph.x the following command is executed
$ mpirun -np 2 $HOME/QE/src/qe-6.4.1/bin/ph.x < h2_ph.in...
and one get the vibrational frequencies in the output fil...
Diagonalizing the dynamical matrix
q = ( 0.000000000 0.000000000 0.000000000 )
*******************************************************...
freq ( 1) = -3.582291 [THz] = -119.49237...
freq ( 2) = -3.582290 [THz] = -119.49234...
freq ( 3) = -3.552544 [THz] = -118.50012...
freq ( 4) = -3.552544 [THz] = -118.50011...
freq ( 5) = -2.974216 [THz] = -99.20917...
freq ( 6) = 131.121910 [THz] = 4373.75613...
*******************************************************...
Negative frequency indicates the imaginary mode. Note tha...
In addition, by using the "dynmat.x" program, vibrational...
The following is the minimalist input file (dynmat.in):
&input
fildyn='h2.dyn'
filout='dynmat.out'
/
By executing the following
$ $HOME/QE/src/qe-6.4.1/bin/dynmat.x < dynmat.in > dynma...
we obtain "dynmat.axsf","dynmat.mold", in which vibration...
When XCrySDen is not available, copy ~ikutaro/QE/tools/ax...
$ cp ~ikutaro/QE/tools/axsf2xsf.sh .
and execute
$ ./axsf2xsf.sh dynmat.axsf
then we get dynmat_#*.xsf for each mode. These file can b...
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