Merge pull request #39 from Crivella/feature-QE

Added demo files for QuantumESPRESSO

.github/workflows/software_repo_native.yml

@@ -15,6 +15,7 @@ jobs:
         - OpenFOAM
         - TensorFlow
         - ESPResSo
+        - QuantumESPRESSO
         EESSI_VERSION:
         - "2023.06"
     steps:

QuantumESPRESSO/README.md

@@ -0,0 +1,8 @@
+# QuantumESPRESSO example
+
+This is an exemplified calculation of the band structure of silicon using QuantumESPRESSO.
+The calculation is performed in two steps: first, a self-consistent field calculation is performed to obtain the charge density, and then a non-self-consistent calculation is performed to obtain the band structure. The assumption is made that the proper convergence tests have already been performed and the lattice parameter has been optimized.
+
+Example re-adapted from https://github.com/Crivella/DFT_QE_beginner_tutorial/tree/master/0_Si_bulk/4_bandstructure
+
+Runtime: ~5 seconds on a single core

QuantumESPRESSO/run.sh

@@ -0,0 +1,204 @@
+if [[ $EESSI_CVMFS_REPO == "/cvmfs/software.eessi.io" ]] && [[ $EESSI_VERSION == "2023.06" ]]; then
+    echo "Running demo for QuantumESPRESSO 7.3.1 ..."
+    module load QuantumESPRESSO/7.3.1-foss-2023a
+    module load gnuplot/5.4.8-GCCcore-12.3.0
+else
+    echo "Don't know which QuantumESPRESSO module to load for ${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}" >&2
+    exit 1
+fi
+
+export OMP_NUM_THREADS=1
+export OMPI_MCA_osc=^ucx
+export OMPI_MCA_btl=^openib,ofi
+export OMPI_MCA_pml=^ucx
+export OMPI_MCA_mtl=^ofi
+
+if [ ! -f Si.pz-vbc.UPF ]; then
+    curl -OL http://pseudopotentials.quantum-espresso.org/upf_files/Si.pz-vbc.UPF
+fi
+
+PSEUDO_DIR=$(pwd)
+TMP_DIR=$(pwd)/tmp
+RUN_COMMAND=""
+
+echo "Parallel command:" $RUN_COMMAND
+echo "Started at: " `date`
+
+############################################################3
+# Calculate the SCF charge density
+
+IN=si_script.scf.in
+OUT=si.scf.out
+cat > $IN << EOF
+&CONTROL
+  calculation  = "scf",
+  prefix       = "Si",
+  pseudo_dir   = "$PSEUDO_DIR",
+  outdir       = "$TMP_DIR",
+  restart_mode = "from_scratch"
+  tprnfor = .true.
+  wf_collect=.true.
+/
+&SYSTEM
+  ibrav     = 2,
+  celldm(1) = 10.21,
+  nat       = 2,
+  ntyp      = 1,
+  ecutwfc   = 20
+  nbnd      = 5
+/
+&ELECTRONS
+  conv_thr    = 1.D-8,
+  mixing_beta = 0.7D0	,
+/
+ATOMIC_SPECIES
+ Si  28.086  Si.pz-vbc.UPF
+ATOMIC_POSITIONS
+ Si 0.00 0.00 0.00
+ Si 0.25 0.25 0.25
+K_POINTS 
+  10
+   0.1250000  0.1250000  0.1250000   1.00
+   0.1250000  0.1250000  0.3750000   3.00
+   0.1250000  0.1250000  0.6250000   3.00
+   0.1250000  0.1250000  0.8750000   3.00
+   0.1250000  0.3750000  0.3750000   3.00
+   0.1250000  0.3750000  0.6250000   6.00
+   0.1250000  0.3750000  0.8750000   6.00
+   0.1250000  0.6250000  0.6250000   3.00
+   0.3750000  0.3750000  0.3750000   1.00
+   0.3750000  0.3750000  0.6250000   3.00
+EOF
+
+echo -e "\tStart: " `date`
+COMMAND="  $RUN_COMMAND pw.x"
+echo -e "\t\t$COMMAND < $IN > $OUT"
+$COMMAND < $IN > $OUT
+echo -e "\tEnd: " `date`
+
+############################################################3
+# Calculate the bands
+
+IN=si_script.bands.in
+OUT=si.bands.out
+cat > $IN << EOF
+&CONTROL
+  calculation  = "bands",
+  prefix       = "Si",
+  pseudo_dir   = "$PSEUDO_DIR",
+  outdir       = "$TMP_DIR",
+  tprnfor = .true.
+  wf_collect=.true.
+/
+&SYSTEM
+  ibrav     = 2,
+  celldm(1) = 10.21,
+  nat       = 2,
+  ntyp      = 1,
+  ecutwfc   = 20
+  nbnd      = 8 
+/
+&ELECTRONS
+  conv_thr    = 1.D-8,
+  mixing_beta = 0.7D0	,
+/
+ATOMIC_SPECIES
+ Si  28.086  Si.pz-vbc.UPF
+ATOMIC_POSITIONS
+ Si 0.00 0.00 0.00
+ Si 0.25 0.25 0.25
+K_POINTS {tpiba_b}
+  6
+    0.500 0.500 0.500 8 ! L
+    0.000 0.000 0.000 8 ! Gamma
+    0.000 1.000 0.000 8 ! X
+    0.250 1.000 0.250 1 ! U
+    0.750 0.750 0.000 8 ! K
+    0.000 0.000 0.000 1 ! Gamma
+EOF
+
+echo -e "\tStart: " `date`
+COMMAND="  $RUN_COMMAND pw.x"
+echo -e "\t\t$COMMAND < $IN > $OUT"
+$COMMAND < $IN > $OUT
+echo -e "\tEnd: " `date`
+
+############################################################3
+# Post-processing
+
+IN=si_script.bandspp.in
+OUT=si.bandspp.out
+cat > $IN << EOF
+&bands
+    prefix = "Si",
+    outdir='$TMP_DIR'
+    filband='Sibands.dat'
+    lsym=.true.
+ /
+EOF
+
+echo -e "\tStart: " `date`
+COMMAND="  $RUN_COMMAND bands.x"
+echo -e "\t\t$COMMAND < $IN > $OUT"
+$COMMAND < $IN > $OUT
+echo -e "\tEnd: " `date`
+
+
+IN=si_script.plotband.in
+OUT=si.plotband.out
+cat > $IN << EOF
+Sibands.dat
+-6.0 10.0
+
+Sibands.ps
+6.377
+1 6.377
+EOF
+
+echo -e "\tStart: " `date`
+COMMAND="plotband.x"
+echo -e "\t\t$COMMAND < $IN > $OUT"
+$COMMAND < $IN > $OUT
+echo -e "\tEnd: " `date`
+
+echo "Run completed at: " `date`
+
+rm -rf $TMP_DIR
+
+############################################################3
+# Plotting the bands
+
+IN=Sibands.gnuplot
+cat > $IN << EOF
+set title "Si band structure from Sibands.dat.gnu"
+#high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   0.0000
+#high-symmetry point:  0.0000 0.0000 0.0000   x coordinate   0.8660
+#high-symmetry point:  0.0000 1.0000 0.0000   x coordinate   1.8660
+#high-symmetry point:  0.2500 1.0000 0.2500   x coordinate   2.2196
+#high-symmetry point:  0.7500 0.7500 0.0000   x coordinate   2.2196
+#high-symmetry point:  0.0000 0.0000 0.0000   x coordinate   3.2802
+L=0.0000
+G1=0.8660
+X=1.8660
+U=2.2196
+G2=3.2802
+set xtics ("L" L,"{/Symbol G}" G1,"X" X,"U,K" U,"{/Symbol G}" G2) nomirror
+set xrange [*:*]
+set yrange [-13:4]
+set grid x
+set ylabel "Energy (eV)"
+set nokey
+EF = 6.377
+set term pngcairo
+set out "Sibands-nosym.png"
+plot "Sibands.dat.gnu" u 1:(\$2-EF) with linespoints pointtype 7 pointsize 0.5,\
+	0 t "" w l lt 2
+set term dumb size 120,40
+set out 
+replot
+EOF
+
+echo -e "\tRunning gnuplot script: " `date`
+gnuplot -p Sibands.gnuplot
+
+exit