第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Visualization of molecular orbitals of a water monomer ...
In this tutorial, how to visualize the electron (charge) ...
We use a water molecule (H2O) in a large box.
** Prep [#ya703441]
If pp.x is not found in the bin/ directory, type
$ make pp
in the root directory.
** SCF/geometry optimization [#k847656e]
First of all, we perform an SCF calculation or geometry o...
Below is the input file (h2o_relax.in) for the geometry o...
H2O in a box
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'h2o'
pseudo_dir = '/home/ikutaro/QE/pseudo/'
outdir = './tmp/'
forc_conv_thr = 1.0D-4
/
&system
ibrav = 1
celldm(1) = 20.00
nat = 3
ntyp = 2
ecutwfc = 50.0
ecutrho = 400.0
nbnd = 8
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
H 0.0000 H.pbe-kjpaw_psl.1.0.0.UPF
O 0.0000 O.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (bohr)
H 1.447909955222 0.000000000000 1.127167...
H -1.447909955222 0.000000000000 1.127167...
O 0.000000000000 0.000000000000 0.000000...
K_POINTS (GAMMA)
Execute pw.x:
$ mpirun -np 4 ${HOME}/QE/src/qe-6.6/bin/pw.x < h2_relax...
or submit a job by using a job script, say, h2o.sh
$ qsub h2o.sh
After the convergence, we obtain the wave functions and c...
** Postprocessing [#l8b85e55]
*** Electron density in real space [#u7eb85da]
Let us plot the electron density in real space.
Input file (pp_rho.in) for pp.x looks like:
&inputpp
prefix = 'h2o'
outdir = './tmp/'
filplot = 'h2o'
plot_num = 0
/
&plot
iflag = 3
output_format = 5
fileout = 'h2o_rho.xsf'
/
NOTE: prefix and outdir should be consistent with the pre...
In this example we set
plot_num = 0
in &inputpp ... / to plot the electron density in real sp...
and
iflag = 3
to plot the density in 3D.
Further, we choose to dump the density in the XSF format ...
output_format = 5
The data is written to 'h2o_rho.xsf` by setting
fileout = 'h2o_rho.xsf'
Execute
$ mpirun -np 4 ${HOME}/QE/src/qe-6.6/bin/pp.x < pp_rho.i...
or alike.
Note that the number of CPUs used for pp.x should be the ...
*** Wave functions [#z3970fc6]
Here let us plot the wave functions, actually, the electr...
Input file for pp.x (pp_psi2.in) looks like:
&inputpp
prefix = 'h2o'
outdir = './tmp/'
filplot = 'h2o'
plot_num = 7
kpoint(1) = 1
kband(1) = 1
kband(2) = 5
lsign = .true.
/
&plot
iflag = 3
output_format = 5
fileout ='.xsf'
/
We use kpoint(1) and kpoint(2) to specify the initial and...
We also use kband(1) and kband(2) to specify the initial ...
At the Gamma-point, we can add the sign by setting lsign ...
NOTE: For the wave function plot, the variable fileout is...
By executing pp.x using this input you may obtain the wav...
h2o_K001_B001.xsf h2o_K001_B002.xsf h2o_K001_B003.xsf ...
終了行:
* Visualization of molecular orbitals of a water monomer ...
In this tutorial, how to visualize the electron (charge) ...
We use a water molecule (H2O) in a large box.
** Prep [#ya703441]
If pp.x is not found in the bin/ directory, type
$ make pp
in the root directory.
** SCF/geometry optimization [#k847656e]
First of all, we perform an SCF calculation or geometry o...
Below is the input file (h2o_relax.in) for the geometry o...
H2O in a box
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'h2o'
pseudo_dir = '/home/ikutaro/QE/pseudo/'
outdir = './tmp/'
forc_conv_thr = 1.0D-4
/
&system
ibrav = 1
celldm(1) = 20.00
nat = 3
ntyp = 2
ecutwfc = 50.0
ecutrho = 400.0
nbnd = 8
/
&electrons
mixing_beta = 0.5
conv_thr = 1.0d-10
/
&ions
/
ATOMIC_SPECIES
H 0.0000 H.pbe-kjpaw_psl.1.0.0.UPF
O 0.0000 O.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (bohr)
H 1.447909955222 0.000000000000 1.127167...
H -1.447909955222 0.000000000000 1.127167...
O 0.000000000000 0.000000000000 0.000000...
K_POINTS (GAMMA)
Execute pw.x:
$ mpirun -np 4 ${HOME}/QE/src/qe-6.6/bin/pw.x < h2_relax...
or submit a job by using a job script, say, h2o.sh
$ qsub h2o.sh
After the convergence, we obtain the wave functions and c...
** Postprocessing [#l8b85e55]
*** Electron density in real space [#u7eb85da]
Let us plot the electron density in real space.
Input file (pp_rho.in) for pp.x looks like:
&inputpp
prefix = 'h2o'
outdir = './tmp/'
filplot = 'h2o'
plot_num = 0
/
&plot
iflag = 3
output_format = 5
fileout = 'h2o_rho.xsf'
/
NOTE: prefix and outdir should be consistent with the pre...
In this example we set
plot_num = 0
in &inputpp ... / to plot the electron density in real sp...
and
iflag = 3
to plot the density in 3D.
Further, we choose to dump the density in the XSF format ...
output_format = 5
The data is written to 'h2o_rho.xsf` by setting
fileout = 'h2o_rho.xsf'
Execute
$ mpirun -np 4 ${HOME}/QE/src/qe-6.6/bin/pp.x < pp_rho.i...
or alike.
Note that the number of CPUs used for pp.x should be the ...
*** Wave functions [#z3970fc6]
Here let us plot the wave functions, actually, the electr...
Input file for pp.x (pp_psi2.in) looks like:
&inputpp
prefix = 'h2o'
outdir = './tmp/'
filplot = 'h2o'
plot_num = 7
kpoint(1) = 1
kband(1) = 1
kband(2) = 5
lsign = .true.
/
&plot
iflag = 3
output_format = 5
fileout ='.xsf'
/
We use kpoint(1) and kpoint(2) to specify the initial and...
We also use kband(1) and kband(2) to specify the initial ...
At the Gamma-point, we can add the sign by setting lsign ...
NOTE: For the wave function plot, the variable fileout is...
By executing pp.x using this input you may obtain the wav...
h2o_K001_B001.xsf h2o_K001_B002.xsf h2o_K001_B003.xsf ...
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