Note on narval 64 processors nodes are used to run these jobs while 48 processors nodes are for GPU users only! To install phonopy v2.17 and alm2.0.0_dev.2 which includes temperature dependent randomn displacements Do: module load StdEnv/2020 gcc/9.3.0 alm/2.0.0_dev.2 python/3.10 virtualenv ~/my_venv pip install phonopy==2.17.0 --no-index Check installation pip list Package Version --------------- -------------------- alm 1.4.0 phonopy 2.17.0+computecanada Exemplary batch job for using phonopy 2.17.0 random on narval in /home/szpunarb/scratch/projectsscratchJan11/QEphonopy/ThNrandomphon/rd300full mkdir rd && cd rd creates dir rd and go there cp required files forces and unit cell: cp /home/szpunarb/scratch/QEphonopy/ThNrandomphon/FORCE_SETS . [szpunarb@narval4 rd]$ cp /home/szpunarb/scratch/QEphonopy/ThNrandomphon/header.in . [szpunarb@narval4 rd]$ cp /home/szpunarb/scratch/QEphonopy/ThNrandomphon/ThN.in . [szpunarb@narval4 rd]$ ls FORCE_SETS header.in ThN.in Create rd.conf file: [szpunarb@narval4 rd]$ cat < rd.conf > CREATE_DISPLACEMENTS = .TRUE. > DIM = 2 2 2 > PRIMITIVE_AXES = AUTO > RANDOM_DISPLACEMENTS = 1000 > RANDOM_DISPLACEMENT_TEMPERATURE = 300 > FC_SYMMETRY = .TRUE. > EOL Note not included above FC_CALCULATOR = ALM [szpunarb@narval4 rd]$ ls FORCE_SETS header.in rd.conf ThN.in create random displacements in unit cell for 300K using batch job phonopydisprandom.sh, pnopy v.2.17: #!/bin/bash -l #SBATCH --job-name=QE_ThN #SBATCH --account=rrg-szpunarb-ad #SBATCH --nodes=1 #SBATCH --tasks-per-node=1 #SBATCH --mem=0 #SBATCH --time=1:00:00 # Load the modules: module load StdEnv/2020 gcc/9.3.0 alm/2.0.0_dev.2 python/3.10 virtualenv ~/my_venv phonopy --qe -c ThN.in -- rd.conf Prepare directories for each file to run QE (does not matter what phonopy version, used old v 2.15 vi phonpyprepfc2fc3QE.sh ... #To copy the header to the created supercells for i in $( seq 100 ); do n=$(printf %03d $i); cat header.in supercell-$n.in >|ThN-$n; done #To make seperate directories for the inputs (supercells) in order to run corresponding scf calculations mkdir disp-{001..100} #Copy the ThN-xxxxx files to created subdirectories above for i in $( seq 100); do n=$(printf %03d $i); cp ThN-$n disp-$n/ThN.in; done Run QE calculations using array: vi jobscfforarraysubmitt.sh #!/bin/bash -l #SBATCH --job-name=QE_ThN #SBATCH --account=rrg-szpunarb-ad #SBATCH --nodes=1 #SBATCH --tasks-per-node=48 #SBATCH --mem=0 #SBATCH --array=001-100 #SBATCH --time=00-48:00 # Load the modules: module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 quantumespresso/6.8 i=$(printf %03d $SLURM_ARRAY_TASK_ID) cd disp-$i srun pw.x < ThN.in > ThN.out Collect results to calculate FORCE_SETS vi phonpycollectfc2v2.17.sh #!/bin/bash -l #SBATCH --job-name=QE_ThN #SBATCH --account=def-szpunarb #SBATCH --nodes=1 #SBATCH --tasks-per-node=48 #SBATCH --mem=0 #SBATCH --time=48:00:00 # Load the modules: module load StdEnv/2020 gcc/9.3.0 alm/2.0.0_dev.2 python/3.10 virtualenv ~/my_venv #create FORCE_SETS in phonopy phonopy -f disp-{001..100}/ThN.out Calculate FORCE_CONTANTS using ALM: vi phonpyFC_ALMrandom.sh # Load the modules: module load StdEnv/2020 gcc/9.3.0 alm/2.0.0_dev.2 python/3.10 virtualenv ~/my_venv phonopy --alm --writefc To calculate DOS for phonons at 300K: run: vi phonpyphononsrandom.sh #!/bin/bash -l #SBATCH --job-name=QE_ThN #SBATCH --account=rrg-szpunarb-ad #SBATCH --nodes=1 #SBATCH --tasks-per-node=1 #SBATCH --mem=0 #SBATCH --time=2:00:00 # Load the modules: module load StdEnv/2020 gcc/9.3.0 alm/2.0.0_dev.2 python/3.10 virtualenv ~/my_venv phonopy --readfc --mesh 50 50 50 -p total_dos.dat was calculatedat 300 K