Exercise-13

Exercises/Exercise-11/Solutions-11.ipynb

@@ -180,7 +180,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.7.0"
   }
  },
  "nbformat": 4,

Exercises/Exercise-11/TASK_0/done/pw.in

+ &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
+1 1 1 0 0 0

Exercises/Exercise-11/TASK_0/run

+#!/bin/bash --login
+#SBATCH --job-name="TASK_0"
+#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
+
+#======START=====
+
+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
+1 1 1 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

Exercises/Exercise-11/TASK_0b/done/pw.in

+ &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
+2 2 2 0 0 0

Exercises/Exercise-11/TASK_0b/run

+#!/bin/bash --login
+#SBATCH --job-name="TASK_0b"
+#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 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

Exercises/Exercise-11/TASK_0c/done/pw.in

+ &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
+2 2 2 1 1 1

Exercises/Exercise-11/TASK_0c/run

+#!/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

Exercises/Exercise-11/TASK_1/done/pw.in

+ &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

Exercises/Exercise-11/TASK_1/run

+#!/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

Exercises/Exercise-11/TASK_3/plot_qe_bands.py

+#!/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