From 521ccee0ced13cf557b801b50f84350b4187aae0 Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Tue, 10 Dec 2024 12:04:32 +0100 Subject: [PATCH] Restore run.sh (updated version). --- examples/pyridineDensOverlap/run.sh | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100755 examples/pyridineDensOverlap/run.sh diff --git a/examples/pyridineDensOverlap/run.sh b/examples/pyridineDensOverlap/run.sh new file mode 100755 index 0000000..71dc8a1 --- /dev/null +++ b/examples/pyridineDensOverlap/run.sh @@ -0,0 +1,18 @@ +echo "======= STEP 1 : Download the sample and tip files." +wget https://zenodo.org/records/14222456/files/pyridine.zip?download=1 -O sample.zip +wget https://zenodo.org/records/14222456/files/CO_tip.zip?download=1 -O tip.zip + +echo "======= STEP 2 : Unzip the sample and tip files." +unzip sample.zip +unzip tip.zip -d tip + +echo "======= STEP 3 : Generate force field grid." +ppafm-conv-rho -s CHGCAR.xsf -t tip/density_CO.xsf -B 1.0 -E +ppafm-generate-elff -i LOCPOT.xsf --tip_dens tip/density_CO.xsf --Rcore 0.7 -E --doDensity +ppafm-generate-dftd3 -i LOCPOT.xsf --df_name PBE + +echo "======= STEP 4 : Relax Probe Particle using that force field grid." +ppafm-relaxed-scan -k 0.25 -q 1.0 --noLJ --Apauli 18.0 --bDebugFFtot # Note the --noLJ for loading separate Pauli and vdW instead of LJ force field + +echo "======= STEP 5 : Plot the results." +ppafm-plot-results -k 0.25 -q 1.0 -a 2.0 --df