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Commit 7389f941 authored by spiasko's avatar spiasko
Browse files

ex11 gelöst

parent f88897db
#!/bin/bash --login
#SBATCH --job-name="TASK_0c"
#SBATCH --nodes=1 # the number of ranks (total)
#SBATCH --ntasks-per-node=12 # the number of ranks per node
##SBATCH --ntasks-per-core=1 # enable this if you want hyperthreading
#SBATCH --cpus-per-task=1 # use this for threaded applications
#SBATCH --time=00:10:00
#SBATCH --constraint=gpu
#SBATCH --account=YOUR_ACCOUNT
##SBATCH --partition=normal
#SBATCH --output="c1"
module load daint-gpu
export CRAY_CUDA_MPS=1
module load QuantumESPRESSO/6.3-CrayIntel-18.08
a=5.43
alat=`echo "${a} / 0.529177" | bc -l`
cat >pw.in << EOF
&control
verbosity='high'
calculation='scf'
restart_mode='from_scratch'
prefix='SI'
pseudo_dir = './',
outdir='./'
wf_collect=.true.
/
&system
ibrav=1
celldm(1)=${alat}
nat=8,
ntyp=1,
ecutwfc = 30,
occupations='smearing',
degauss=0.001
/
&electrons
conv_thr = 1.0e-8
mixing_beta = 0.5
/
&ions
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-mt_fhi.UPF
ATOMIC_POSITIONS crystal
Si 0.000000 0.000000 0.000000
Si 0.000000 0.500000 0.500000
Si 0.500000 0.000000 0.500000
Si 0.500000 0.500000 0.000000
Si 0.750000 0.250000 0.750000
Si 0.250000 0.250000 0.250000
Si 0.250000 0.750000 0.750000
Si 0.750000 0.750000 0.250000
K_POINTS automatic
2 2 2 1 1 1
EOF
srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c $SLURM_CPUS_PER_TASK --cpu_bind=rank --hint=nomultithread pw.x <pw.in > si.out
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&control
verbosity='high'
calculation='scf'
restart_mode='from_scratch'
prefix='SI'
pseudo_dir = './',
outdir='./'
wf_collect=.true.
/
&system
ibrav=1
celldm(1)=10.26121694631474912930
nat=8,
ntyp=1,
ecutwfc = 30,
occupations='smearing',
degauss=0.001
/
&electrons
conv_thr = 1.0e-8
mixing_beta = 0.5
/
&ions
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-mt_fhi.UPF
ATOMIC_POSITIONS crystal
Si 0.000000 0.000000 0.000000
Si 0.000000 0.500000 0.500000
Si 0.500000 0.000000 0.500000
Si 0.500000 0.500000 0.000000
Si 0.750000 0.250000 0.750000
Si 0.250000 0.250000 0.250000
Si 0.250000 0.750000 0.750000
Si 0.750000 0.750000 0.250000
K_POINTS automatic
3 3 3 0 0 0
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#!/bin/bash --login
#SBATCH --job-name="TASK_1"
#SBATCH --nodes=1 # the number of ranks (total)
#SBATCH --ntasks-per-node=12 # the number of ranks per node
##SBATCH --ntasks-per-core=1 # enable this if you want hyperthreading
#SBATCH --cpus-per-task=1 # use this for threaded applications
#SBATCH --time=00:10:00
#SBATCH --constraint=gpu
#SBATCH --account=YOUR_ACCOUNT
##SBATCH --partition=normal
#SBATCH --output="c1"
module load daint-gpu
export CRAY_CUDA_MPS=1
module load QuantumESPRESSO/6.3-CrayIntel-18.08
a=5.43
alat=`echo "${a} / 0.529177" | bc -l`
cat >pw.in << EOF
&control
verbosity='high'
calculation='scf'
restart_mode='from_scratch'
prefix='SI'
pseudo_dir = './',
outdir='./'
wf_collect=.true.
/
&system
ibrav=1
celldm(1)=${alat}
nat=8,
ntyp=1,
ecutwfc = 30,
occupations='smearing',
degauss=0.001
/
&electrons
conv_thr = 1.0e-8
mixing_beta = 0.5
/
&ions
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-mt_fhi.UPF
ATOMIC_POSITIONS crystal
Si 0.000000 0.000000 0.000000
Si 0.000000 0.500000 0.500000
Si 0.500000 0.000000 0.500000
Si 0.500000 0.500000 0.000000
Si 0.750000 0.250000 0.750000
Si 0.250000 0.250000 0.250000
Si 0.250000 0.750000 0.750000
Si 0.750000 0.750000 0.250000
K_POINTS automatic
3 3 3 0 0 0
EOF
srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c $SLURM_CPUS_PER_TASK --cpu_bind=rank --hint=nomultithread pw.x <pw.in > si.out
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#!/users/keimre/soft/miniconda3/bin/python
import numpy as np
import xml.etree.ElementTree as et
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import argparse
ang_2_bohr = 1.0/0.52917721067
hart_2_ev = 27.21138602
parser = argparse.ArgumentParser(
description='Plots QE bands.')
parser.add_argument(
'qe_xml',
metavar='FILENAME',
help='QE xml file.')
args = parser.parse_args()
def read_band_data_new_xml(xml_file):
"""
Reads data from QE bands calculations (new XML)
Returns:
- kpts[i_kpt] = [kx, ky, kz] in [2*pi/a]
- eigvals[i_kpt, i_band] in [eV]
- fermi_en in [eV]
"""
data_file_xml = et.parse(xml_file)
data_file_root = data_file_xml.getroot()
output_node = data_file_root.find('output')
# Find fermi
band_node = output_node.find('band_structure')
fermi_en = float(band_node.find('fermi_energy').text)*27.21138602
lsda = band_node.find('spinorbit').text
kpts = []
eigvals = []
for kpt in band_node.findall("ks_energies"):
k_coords = np.array(kpt.find('k_point').text.split(), dtype=float)
kpts.append(k_coords)
eig_vals = np.array(kpt.find('eigenvalues').text.split(), dtype=float)
eigvals.append(eig_vals*27.21138602)
kpts = np.array(kpts)
eigvals = np.array(eigvals)
return kpts, eigvals, fermi_en
kpts, eigvals, fermi_en = read_band_data_new_xml(args.qe_xml)
k_arr = [0.0]
cum_sum = 0.0
for i_k in range(1, len(kpts)):
k0 = kpts[i_k-1]
k1 = kpts[i_k]
dk = k1 - k0
cum_sum += np.linalg.norm(dk)
k_arr.append(cum_sum)
x_ticks = {}
for i_k, kpt in enumerate(kpts):
if np.allclose(kpt, np.array([0.0, 0.0, 0.0])):
x_ticks['G'] = k_arr[i_k]
if np.allclose(kpt, np.array([-0.5, 0.5, 0.5])):
x_ticks['L'] = k_arr[i_k]
if np.allclose(kpt, np.array([0.5, 0.5, 0.5])):
x_ticks['L'] = k_arr[i_k]
if np.allclose(kpt, np.array([-1.0, 0.0, 0.0])):
x_ticks['X'] = k_arr[i_k]
if np.allclose(kpt, np.array([0.5, 0.0, 0.5])):
x_ticks['X'] = k_arr[i_k]
plt.figure(figsize=(6, 10))
plt.plot(k_arr, eigvals, 'b', lw=2.0)
plt.xlim([0.0, np.max(k_arr)])
plt.ylim([np.min(eigvals), np.max(eigvals)])
plt.xticks(list(x_ticks.values()), list(x_ticks.keys()))
for xtick in list(x_ticks.values()):
plt.axvline(xtick, color='gray')
plt.ylabel("energy [eV]")
plt.savefig("./bands.png", dpi=200)
\ No newline at end of file
&control
verbosity='high'
calculation='scf'
restart_mode='from_scratch'
prefix='SI'
pseudo_dir = './',
outdir='./'
wf_collect=.true.
/
&system
ibrav=2
celldm(1)=10.26121694631474912930
nat=2,
ntyp=1,
ecutwfc = 30,
occupations='smearing',
degauss=0.001
/
&electrons
conv_thr = 1.0e-8
mixing_beta = 0.5
/
&ions
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-mt_fhi.UPF
ATOMIC_POSITIONS crystal
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
8 8 8 1 1 1
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