Example: Water dimer dissociation¶

#!/bin/sh

cp -r "$AMSHOME/examples/infretis/water_dimer/ams_inp" .
cp    "$AMSHOME/examples/infretis/water_dimer/infretis.toml" .

export NSCM=1 # MPI ranks per infretis worker
export OMP_NUM_THREADS=1 # OpenMP threads per MPI rank

# The following retry loop is only needed for regression testing purposes,
# ordinary simulations need just the few lines between "BEGIN infretis run" and
# "END infretis run"
i=0
retry_limit=4
while true; do
# BEGIN infretis run
   cp -r "$AMSHOME/examples/infretis/water_dimer/load" .
   $AMSBIN/uv_scm run infretis exec infretisrun -i infretis.toml
   # -nskip 10 is only needed to make wham work for this extremely short run
   $AMSBIN/uv_scm run infretis exec inft wham -nskip 10
# END infretis run

# What follows is purely regression testing logic
   if awk 'BEGIN { max_Pcross = 0.25; } END { exit(!($2 != 0 && $2 <= max_Pcross && $3 != 0 && $3 <= max_Pcross && $4 != 0 && $4 <= max_Pcross)); }' wham/Pcross.txt; then
      # All Pcross are nonzero => WHAM successfull
      # We also check that Pcross aren't too large, which does happen randomly
      # and would just trigger a spurious diff, so we just retry in that case
      # to see if the diff goes away.
      break
   fi
   if [[ ! -s wham/Pcross.txt ]]; then
      # Something went badly wrong, bail out
      exit 1
   elif ((i++ < retry_limit)); then
      echo "WHAM failed, retrying..."
      rm -rf load/ wham/ worker*/ amsworker_*/ restart.toml infretis_data.txt *.log
   else
      echo "Giving up after $i attempts"
      exit 2
   fi
done
echo "Success, had to retry $i times"

echo "BEGIN pathlengths.txt"
# skip [0-] as that is the least well-defined one
grep -v '^-1' wham/pathlengths.txt
echo "END pathlengths.txt"

for f in wham/{ploc_unscaled,Pcross}.txt; do
   echo "BEGIN ${f#*/}"
   cat "$f"
   echo "END ${f#*/}"
done

echo "BEGIN overall Pcross"
tail -n 1 wham/Pcross.txt
echo "END overall Pcross"