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weiol authored Apr 7, 2024
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* An introductory example for working with VASP
* In general, examples are chosen for fast calculation
* Use different job scripts, submit to the Slurm job scheduler (Tetralith) or run interactively (MeluXina)
* Use different job scripts, submit to the Slurm job scheduler on Tetralith or LEONARDO
* Use VASP, gnuplot, python, ASE
* bash shell scripts

Expand All @@ -17,30 +17,30 @@ Select instructions for the system you are using:
Instructions for use on the NAISS cluster Tetralith (NSC)
```
```{group-tab} MeluXina
Instructions for use on the EuroHPC cluster MeluXina
```{group-tab} LEONARDO
Instructions for use on the EuroHPC cluster LEONARDO
```
````
`````

First, copy the example folder which contains the input files INCAR, POSCAR, KPOINTS and some useful scripts
````{tabs}
```{group-tab} Tetralith
cp -r /software/sse/manual/vasp/training/ws2023/fcc_Si .
cp -r /software/sse2/tetralith_el9/manual/vasp/training/ws2024/fcc_Si .
cd fcc_Si
also copy the latest POTCAR (PBE GGA) file for Si
cp /software/sse/manual/vasp/POTCARs/PBE/2015-09-21/Si/POTCAR .
cp /software/sse2/tetralith_el9/manual/vasp/POTCARs/PBE/2024-03-19/Si/POTCAR .
```
```{group-tab} MeluXina
cp -r /project/home/p200051/vasp_ws2023/examples/fcc_Si .
```{group-tab} LEONARDO
cp -r /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/examples/fcc_Si .
cd fcc_Si
also copy the latest POTCAR (PBE GGA) file for Si
cp /project/home/p200051/vasp_ws2023/vasp/potpaw_PBE.54/Si/POTCAR .
cp /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/potpaw_PBE.64/Si/POTCAR .
```
````

Expand Down Expand Up @@ -142,36 +142,46 @@ A first static calculation for Si with the lattice constant 3.9 Å. Create a new
cp -r scf0 scf1
cd scf0

````{tabs}
```{group-tab} Tetralith
Submit the job script "run.sh" to the job queue with
Submit the job script "run.sh" to the job queue with

sbatch run.sh
sbatch run.sh

The job script looks like below
The job script looks like below

````{tabs}
```{group-tab} Tetralith
#!/bin/bash
#SBATCH -A naiss2023-22-205
#SBATCH -A naiss2024-22-241
#SBATCH -t 0:30:00
#SBATCH -n 4
#SBATCH -J vaspjob
module load VASP/6.4.0.14022023-omp-nsc1-intel-2018a-eb
module load VASP/6.4.3.19032024-omp-hpc1-intel-2023a-eb
mpprun vasp_std
```
```{group-tab} MeluXina
Run the job interactively in the Jupyter-notebook terminal with
srun --hint=nomultithread -n 8 vasp_std
This works if the settings were applied previously, see [starting section](../meluxina)
source /project/home/p200051/vasp_ws2023/setup.sh
which set the path to VASP binaries and loads the corresponding modules it was built with, check e.g. with "cat"
```{group-tab} LEONARDO
#!/bin/bash
#SBATCH -A EUHPC_D02_030
#SBATCH -p boost_usr_prod
#SBATCH --qos=boost_qos_dbg
#SBATCH --time 00:15:00
#SBATCH -n 8
#SBATCH --ntasks-per-node=8
#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 load intel-oneapi-compilers/2023.2.1
module load intel-oneapi-mpi/2021.10.0
module load intel-oneapi-mkl/2023.2.0
module load hdf5/1.14.3--intel-oneapi-mpi--2021.10.0--oneapi--2023.2.0
export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
export OMP_NUM_THREADS=1
srun vasp_std
cat /project/home/p200051/vasp_ws2023/setup.sh
```
````

Expand All @@ -190,7 +200,7 @@ in which `JOBID` is a string of numbers. Note that
* Some warning messages will only show in the standard output of the job, `slurm-JOBID.out` if submitted to the queue.
**Therefore, also carefully check the output when running interactively.**

You can quickly check the iteration steps and convergence with "cat", in a different terminal if it's still running interactively
You can quickly check the iteration steps and convergence with "cat"

cat OSZICAR

Expand All @@ -214,19 +224,19 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3
````{tabs}
```{group-tab} Tetralith
#!/bin/bash
#SBATCH -A naiss2023-22-205
#SBATCH -A naiss2024-22-241
#SBATCH -t 0:30:00
#SBATCH -n 4
#SBATCH -J vaspjob
module load VASP/6.3.0.20012022-omp-nsc1-intel-2018a-eb
module load VASP/6.4.3.19032024-omp-hpc1-intel-2023a-eb
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 /software/sse/manual/vasp/POTCARs/PBE/2015-09-21/Si/POTCAR .
cp /software/sse/manual/vasp/training/ws2023/fcc_Si/INCAR .
cp /software/sse/manual/vasp/training/ws2023/fcc_Si/KPOINTS .
cp /software/sse2/tetralith_el9/manual/vasp/POTCARs/PBE/2024-03-19/Si/POTCAR .
cp /software/sse2/tetralith_el9/manual/vasp/training/ws2024/fcc_Si/INCAR .
cp /software/sse2/tetralith_el9/manual/vasp/training/ws2024/fcc_Si/KPOINTS .
cat >POSCAR <<EOF
fcc:
$i
Expand All @@ -243,16 +253,33 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3
cd ..
done
```
```{group-tab} MeluXina
```{group-tab} LEONARDO
#!/bin/bash
#SBATCH -A EUHPC_D02_030
#SBATCH -p boost_usr_prod
#SBATCH --qos=boost_qos_dbg
#SBATCH --time 00:15:00
#SBATCH -n 8
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1
#SBATCH --job-name=vaspjob
source /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/VASP-6.4.3-cpu1.sh
module load intel-oneapi-compilers/2023.2.1
module load intel-oneapi-mpi/2021.10.0
module load intel-oneapi-mkl/2023.2.0
module load hdf5/1.14.3--intel-oneapi-mpi--2021.10.0--oneapi--2023.2.0
export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
export OMP_NUM_THREADS=1
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 /project/home/p200051/vasp_ws2023/vasp/potpaw_PBE.54/Si/POTCAR .
cp /project/home/p200051/vasp_ws2023/examples/fcc_Si/INCAR .
cp /project/home/p200051/vasp_ws2023/examples/fcc_Si/KPOINTS .
cat >POSCAR <<EOF
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 .
cat >POSCAR <<!
fcc:
$i
0.5 0.5 0.0
Expand All @@ -262,8 +289,8 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3
1
cartesian
0 0 0
EOF
srun --hint=nomultithread -n 8 vasp_std
!
srun vasp_std
E=`awk '/F=/ {print $0}' OSZICAR` ; echo $i $E >>../SUMMARY.fcc
cd ..
done
Expand All @@ -272,14 +299,10 @@ In this part we will calculate the total energies of fcc Si between 3.5 and 4.3

In brief, the above script creates a new folder with the same name as the lattice constant, copying POTCAR, INCAR and KPOINTS, while creating a new POSCAR file. It also collects the total energies from all OSZICAR files into a new file "SUMMARY.fcc".

Now, submit the job script "run-vol.sh" to the queue (Tetralith)
Now, submit the job script "run-vol.sh" to the queue

sbatch run-vol.sh

or run it as an interactive job (MeluXina)

./run-vol.sh

After a successful run, there should now be folders 3.5 - 4.3 with the different calculations and a file SUMMARY.fcc which can be checked e.g. with "less" or "cat"

3.5 1 F= -.44256909E+01 E0= -.44234194E+01 d E =-.454310E-02
Expand All @@ -292,14 +315,14 @@ After a successful run, there should now be folders 3.5 - 4.3 with the different
4.2 1 F= -.46937300E+01 E0= -.46922884E+01 d E =-.288335E-02
4.3 1 F= -.45831536E+01 E0= -.45812206E+01 d E =-.386597E-02

You can make a quick plot of the total energy as a function of the lattice constant, e.g. by using gnuplot. First, load the module
You can make a quick plot of the total energy as a function of the lattice constant, e.g. by using gnuplot. First, load the module (Tetralith)

````{tabs}
```{group-tab} Tetralith
module load gnuplot/5.2.2-nsc1
module load gnuplot/5.4.4-hpc1-gcc-2022a-eb
```
```{group-tab} MeluXina
module load gnuplot/5.4.4-GCCcore-11.3.0
```{group-tab} LEONARDO
gnuplot is already available in the path
```
````
and start it with
Expand All @@ -312,12 +335,14 @@ thereafter, at the "gnuplot>" prompt type
```{group-tab} Tetralith
plot "SUMMARY.fcc" using ($1):($4) w lp
```
```{group-tab} MeluXina
```{group-tab} LEONARDO
set term png
set output "SUMMARY.fcc.png"
plot "SUMMARY.fcc" using ($1):($4) w lp
Thereafter, open the output file `SUMMARY.fcc.png` in Jupyter-notebook.
Thereafter, copy the file `SUMMARY.fcc.png` to your local computer, open a terminal using "scp"
scp [email protected]:/your/path/fcc_Si/SUMMARY.fcc.png .
```
````

Expand All @@ -329,22 +354,19 @@ To find a more exact value, we can use an equation of state method. For example,
```{group-tab} Tetralith
First, we need to load ASE and a suitable Python3 module,
module load ASE/3.21.0-nsc1
module load Python/3.10.4-env-nsc1-gcc-2022a-eb
module load ASE/3.22.1-hpc1-python
module load Python/3.10.4-env-hpc1-gcc-2022a-eb
```
```{group-tab} MeluXina
Using py4vasp, ASE is already included as a dependency and therefore directly available. However, since the terminal was used for running VASP interactively, meaning that a different set of modules were loaded with `source /project/home/p200051/vasp_ws2023/setup.sh`), it will not work immediately in the same terminal.
```{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:
source /leonardo_scratch/fast/EUHPC_D02_030/vasp_ws2024/py4vasp.sh
* The fastest way to fix this is to open up a new terminal in Jupyter-notebook for just running ASE in the terminal.
To check all packages included with the Python environment, one can type:
* Alternatively, load the correct dependecies to use the Python
pip list
module load Python/3.10.4-GCCcore-11.3.0
after finishing with ASE, to continue to run VASP interactively, again apply
source /project/home/p200051/vasp_ws2023/setup.sh
```
````

Expand Down Expand Up @@ -390,7 +412,7 @@ and produces the file "vol_etot.dat". We will use a small python script "eqos.py
print ("B: %2.6f GPa" % (B/GPa))
print ()

run it to calculate the equilibrium volume using an equation of state
run it to calculate the equilibrium volume using an equation of state (first loading the modules or activating the environment, as described above)

python eqos.py

Expand Down Expand Up @@ -430,14 +452,10 @@ and insert the lattice parameter **a** obtained in **2.** by editing POSCAR, e.g

vi POSCAR

or use your favourite text editor (`emacs`, `nano`, `gedit`, ...). Finally, submit the job (Tetralith)
or use your favourite text editor (`emacs`, `nano`, `gedit`, ...). Finally, submit the job

sbatch run.sh

or run it interactively (MeluXina)

srun --hint=nomultithread -n 8 vasp_std

and compare the total energy with previous results. For example, try

grep "free energy" OUTCAR
Expand All @@ -454,4 +472,3 @@ and compare the total energy with previous results. For example, try
* Try different methods to compute the equilibrium by editing the script "eqos.py"

* Compute the equilibrium volumes for a less dense k-mesh `5 5 5` in KPOINTS and with ENCUT set to ENMIN from POTCAR, and (2) for a denser k-mesh `29 29 29` and with ENCUT = ENMAX x 1.3. Suggestion: create new folders, copy and edit the "run_vol.sh" job script

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