vasp_rundef.sh (runs VASP locally)

#!/bin/bash
nohup mpirun -np 30 /opt/vasp/vasp.6.5.0/bin/vasp_std > vasp.out 2>&1 &

phono3pydispfc2fc3.sh (generate displacements)

#!/bin/bash
source /data/phonopy/phonopy_env/bin/activate
phono3py -d --dim="2 2 2" -c POSCAR
# For cutoff-based reduced displacements, use:
# phono3py --cutoff-pair=2 -d --dim-fc2="2 2 2" --dim="2 2 2" -c POSCAR
deactivate

phono3pyprepfc2fc3.sh (create displacement folders)

#!/bin/bash
P=$PWD
for i in $(ls POSCAR-0* | sed 's/POSCAR-//'); do
  mkdir disp-$i
  cd disp-$i
  cp ../POSCAR-$i POSCAR
  cp ../INCAR ../POTCAR ../KPOINTS ../vasp_rundef.sh .
  cd ..
done

submitdispxxxfc2fc3.sh (launch all VASP jobs)

#!/bin/bash
for i in $(ls POSCAR-0* | sed 's/POSCAR-//'); do
  cd disp-$i
  bash vasp_rundef.sh
  echo "Submitted disp-$i"
  cd ..
done

phono3pycollectfc2fc3.sh (collect FC2 and FC3)

#!/bin/bash
source /data/phonopy/phonopy_env/bin/activate

# Generate list of FC3 vasprun.xml paths
for i in $(ls POSCAR-0* | sed 's/POSCAR-//'); do
  echo "disp-$i/vasprun.xml"
done > file_list.dat

# Generate FC3 and FC2
phono3py --cf3-file file_list.dat
phono3py --cf2 disp-*/vasprun.xml

deactivate

phono3pyhdffc2fc3.sh (generate FORCE_SETS / hdf5)

#!/bin/bash
source /data/phonopy/phonopy_env/bin/activate
phono3py --dim="2 2 2" -c POSCAR
deactivate

phono3pythconductsig444.sh (calculate conductivity)

#!/bin/bash
source /data/phonopy/phonopy_env/bin/activate

# Example: Thermal conductivity with 4×4×4 mesh and Brillouin zone integration
phono3py --fc3 --fc2 --dim="2 2 2" --mesh="4 4 4" -c POSCAR --br

# Optional: Try other meshes
# phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --br

deactivate

Execution Order on Workstation

You can run everything manually like this:

chmod +x phono3pydispfc2fc3.sh
./phono3pydispfc2fc3.sh
chmod +x phono3pyprepfc2fc3.sh
./phono3pyprepfc2fc3.sh
chmod +x submitdispxxxfc2fc3.sh   # Wait until all VASP jobs finish
./submitdispxxxfc2fc3.sh
chmod +x phono3pycollectfc2fc3.sh
./phono3pycollectfc2fc3.sh
chmod +x phono3pyhdffc2fc3.sh
./phono3pyhdffc2fc3.sh
chmod +x phono3pythconductsig444.sh
./phono3pythconductsig444.sh