diff --git a/content/fcc_Si.md b/content/fcc_Si.md index d6627fe..aa5edea 100644 --- a/content/fcc_Si.md +++ b/content/fcc_Si.md @@ -35,12 +35,12 @@ First, copy the example folder which contains the input files INCAR, POSCAR, KPO ``` ```{group-tab} LEONARDO - cp -r /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/examples/fcc_Si . + cp -r /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/examples/fcc_Si . cd fcc_Si also copy the latest POTCAR (PBE GGA) file for Si - cp /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/potpaw_PBE.64/Si/POTCAR . + cp /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/potpaw_PBE.64/Si/POTCAR . ``` ```` @@ -162,7 +162,7 @@ The job script looks like below ``` ```{group-tab} LEONARDO #!/bin/bash - #SBATCH -A EUHPC_D02_030 + #SBATCH -A EUHPC_TD02_030 #SBATCH -p boost_usr_prod #SBATCH --qos=boost_qos_dbg #SBATCH --time 00:15:00 @@ -171,7 +171,8 @@ The job script looks like below #SBATCH --cpus-per-task=1 #SBATCH --job-name=vaspjob - source /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/VASP-6.4.3-cpu1.sh + module use /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/modules + module load VASP-6.4.3-cpu1 module load intel-oneapi-compilers/2023.2.1 module load intel-oneapi-mpi/2021.10.0 module load intel-oneapi-mkl/2023.2.0 @@ -255,7 +256,7 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3 ``` ```{group-tab} LEONARDO #!/bin/bash - #SBATCH -A EUHPC_D02_030 + #SBATCH -A EUHPC_TD02_030 #SBATCH -p boost_usr_prod #SBATCH --qos=boost_qos_dbg #SBATCH --time 00:15:00 @@ -264,7 +265,8 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3 #SBATCH --cpus-per-task=1 #SBATCH --job-name=vaspjob - source /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/VASP-6.4.3-cpu1.sh + module use /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/modules + module load VASP-6.4.3-cpu1 module load intel-oneapi-compilers/2023.2.1 module load intel-oneapi-mpi/2021.10.0 module load intel-oneapi-mkl/2023.2.0 @@ -276,9 +278,9 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3 for i in 3.5 3.6 3.7 3.8 3.9 4.0 4.1 4.2 4.3 ; do mkdir -p $i cd $i - cp /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/potpaw_PBE.64/Si/POTCAR . - cp /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/examples/fcc_Si/INCAR . - cp /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/examples/fcc_Si/KPOINTS . + cp /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/potpaw_PBE.64/Si/POTCAR . + cp /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/examples/fcc_Si/INCAR . + cp /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/examples/fcc_Si/KPOINTS . cat >POSCAR <" prompt type set output "SUMMARY.fcc.png" plot "SUMMARY.fcc" using ($1):($4) w lp - Thereafter, copy the file `SUMMARY.fcc.png` to your local computer, open a terminal using "scp" - - scp your-username@login.leonardo.cineca.it:/your/path/fcc_Si/SUMMARY.fcc.png . + Thereafter, copy the file `SUMMARY.fcc.png` to your local computer ``` ```` @@ -359,14 +349,19 @@ To find a more exact value, we can use an equation of state method. For example, ``` ```{group-tab} LEONARDO - Here, a Python environment including ASE has been prepared, which also includes py4vasp, numpy etc. It can be activated by sourcing a script prepared for the workshop: + Here, a Python environment has been prepared for the workshop, which includes ASE, py4vasp, numpy etc. It can be activated by loading the module: - source /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/py4vasp.sh + module use /leonardo_scratch/fast/EUHPC_TD02_030/vasp_ws2024/modules + module load pythonws-env/1.0-hpc1 - To check all packages included with the Python environment, one can type: + To check all packages included with the Python environment, one can e.g. type: pip list + To confirm use of the "correct" python, one can type: + + which python + ``` ````